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PDBsum entry 1a8o
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Viral protein
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PDB id
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1a8o
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PDB id:
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Viral protein
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Title:
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HIV capsid c-terminal domain
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Structure:
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HIV capsid. Chain: a. Fragment: c-terminal domain, residues 151 - 231. Engineered: yes. Mutation: yes
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Source:
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Human immunodeficiency virus 1. Organism_taxid: 11676. Cell_line: bl21. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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Biol. unit:
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Monomer (from PDB file)
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Resolution:
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1.70Å
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R-factor:
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0.215
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R-free:
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0.253
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Authors:
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T.R.Gamble,S.Yoo,F.F.Vajdos,U.K.Von Schwedler,D.K.Worthylake,H.Wang, J.P.Mccutcheon,W.I.Sundquist,C.P.Hill
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Key ref:
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T.R.Gamble
et al.
(1997).
Structure of the carboxyl-terminal dimerization domain of the HIV-1 capsid protein.
Science,
278,
849-853.
PubMed id:
DOI:
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Date:
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27-Mar-98
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Release date:
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14-Oct-98
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Supersedes:
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PROCHECK
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Headers
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References
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P12497
(POL_HV1N5) -
Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate NY5)
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Seq:
Struc:
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1435 a.a.
70 a.a.*
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Key: |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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Enzyme class 1:
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E.C.2.7.7.-
- ?????
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Enzyme class 2:
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E.C.2.7.7.49
- RNA-directed Dna polymerase.
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Reaction:
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
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DNA(n)
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+
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2'-deoxyribonucleoside 5'-triphosphate
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=
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DNA(n+1)
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+
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diphosphate
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Enzyme class 3:
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E.C.2.7.7.7
- DNA-directed Dna polymerase.
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Reaction:
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
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DNA(n)
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+
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2'-deoxyribonucleoside 5'-triphosphate
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=
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DNA(n+1)
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+
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diphosphate
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Enzyme class 4:
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E.C.3.1.-.-
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Enzyme class 5:
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E.C.3.1.13.2
- exoribonuclease H.
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Reaction:
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Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
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Enzyme class 6:
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E.C.3.1.26.13
- retroviral ribonuclease H.
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Enzyme class 7:
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E.C.3.4.23.16
- HIV-1 retropepsin.
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Reaction:
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Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Science
278:849-853
(1997)
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PubMed id:
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Structure of the carboxyl-terminal dimerization domain of the HIV-1 capsid protein.
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T.R.Gamble,
S.Yoo,
F.F.Vajdos,
U.K.von Schwedler,
D.K.Worthylake,
H.Wang,
J.P.McCutcheon,
W.I.Sundquist,
C.P.Hill.
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ABSTRACT
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The carboxyl-terminal domain, residues 146 to 231, of the human immunodeficiency
virus-1 (HIV-1) capsid protein [CA(146-231)] is required for capsid dimerization
and viral assembly. This domain contains a stretch of 20 residues, called the
major homology region (MHR), which is conserved across retroviruses and is
essential for viral assembly, maturation, and infectivity. The crystal
structures of CA(146-231) and CA(151-231) reveal that the globular domain is
composed of four helices and an extended amino-terminal strand. CA(146-231)
dimerizes through parallel packing of helix 2 across a dyad. The MHR is distinct
from the dimer interface and instead forms an intricate hydrogen-bonding network
that interconnects strand 1 and helices 1 and 2. Alignment of the CA(146-231)
dimer with the crystal structure of the capsid amino-terminal domain provides a
model for the intact protein and extends models for assembly of the central
conical core of HIV-1.
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Selected figure(s)
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Figure 3.
Fig. 3. Representative sedimentation profiles of (A) intact
CA, (B) CA(146-231), and (C) CA(M185A) mutant protein. The
analysis reveals that intact CA and CA(146-231) dimerize with
similar affinities (K[d] = 18 ± 1 and 10 ± 3
µM, respectively), but that the CA(M185A) mutation
abolishes dimerization. Theoretical curves for monomer (M) and
monomer/dimer (M/D) distributions are^ shown assuming K[d] = 18
µM (A and C) or 10 µM (B). A[280], absorbance^ at
280 nm.
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Figure 5.
Fig. 5. Model for the intact HIV-1 capsid dimer. The
CA(146-231) dimer (cyan) is shown covalently linked to the
CA(1-151) domain (23). The five disordered residues that connect
the two domains can be modeled to allow ~90° range of
relative rotational orientation for the two domains about the
vertical twofold axis.
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The above figures are
reprinted
by permission from the AAAs:
Science
(1997,
278,
849-853)
copyright 1997.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Engelman,
and
P.Cherepanov
(2012).
The structural biology of HIV-1: mechanistic and therapeutic insights.
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Nat Rev Microbiol,
10,
279-290.
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O.Pornillos,
B.K.Ganser-Pornillos,
and
M.Yeager
(2011).
Atomic-level modelling of the HIV capsid.
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Nature,
469,
424-427.
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PDB codes:
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B.Chen,
and
R.Tycko
(2010).
Structural and dynamical characterization of tubular HIV-1 capsid protein assemblies by solid state nuclear magnetic resonance and electron microscopy.
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Protein Sci,
19,
716-730.
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B.G.Luttge,
and
E.O.Freed
(2010).
FIV Gag: virus assembly and host-cell interactions.
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Vet Immunol Immunopathol,
134,
3.
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C.S.Adamson,
and
E.O.Freed
(2010).
Novel approaches to inhibiting HIV-1 replication.
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Antiviral Res,
85,
119-141.
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E.B.Monroe,
S.Kang,
S.K.Kyere,
R.Li,
and
P.E.Prevelige
(2010).
Hydrogen/deuterium exchange analysis of HIV-1 capsid assembly and maturation.
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Structure,
18,
1483-1491.
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G.N.Llewellyn,
I.B.Hogue,
J.R.Grover,
and
A.Ono
(2010).
Nucleocapsid promotes localization of HIV-1 gag to uropods that participate in virological synapses between T cells.
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PLoS Pathog,
6,
e1001167.
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J.Jung,
I.J.Byeon,
J.Ahn,
J.Concel,
and
A.M.Gronenborn
(2010).
1H, 15N and 13C assignments of the dimeric C-terminal domain of HIV-1 capsid protein.
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Biomol NMR Assign,
4,
21-23.
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K.Kono,
H.Song,
M.Yokoyama,
H.Sato,
T.Shioda,
and
E.E.Nakayama
(2010).
Multiple sites in the N-terminal half of simian immunodeficiency virus capsid protein contribute to evasion from rhesus monkey TRIM5α-mediated restriction.
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Retrovirology,
7,
72.
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M.P.Milev,
C.M.Brown,
and
A.J.Mouland
(2010).
Live cell visualization of the interactions between HIV-1 Gag and the cellular RNA-binding protein Staufen1.
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Retrovirology,
7,
41.
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N.Inagaki,
H.Takeuchi,
M.Yokoyama,
H.Sato,
A.Ryo,
H.Yamamoto,
M.Kawada,
and
T.Matano
(2010).
A structural constraint for functional interaction between N-terminal and C-terminal domains in simian immunodeficiency virus capsid proteins.
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Retrovirology,
7,
90.
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S.B.Kutluay,
and
P.D.Bieniasz
(2010).
Analysis of the initiating events in HIV-1 particle assembly and genome packaging.
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PLoS Pathog,
6,
e1001200.
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S.D.Hicks,
and
C.L.Henley
(2010).
Coarse-grained protein-protein stiffnesses and dynamics from all-atom simulations.
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Phys Rev E Stat Nonlin Soft Matter Phys,
81,
030903.
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S.Misumi,
M.Inoue,
T.Dochi,
N.Kishimoto,
N.Hasegawa,
N.Takamune,
and
S.Shoji
(2010).
Uncoating of human immunodeficiency virus type 1 requires prolyl isomerase Pin1.
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J Biol Chem,
285,
25185-25195.
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T.Wu,
S.A.Datta,
M.Mitra,
R.J.Gorelick,
A.Rein,
and
J.G.Levin
(2010).
Fundamental differences between the nucleic acid chaperone activities of HIV-1 nucleocapsid protein and Gag or Gag-derived proteins: biological implications.
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Virology,
405,
556-567.
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V.Krishna,
G.S.Ayton,
and
G.A.Voth
(2010).
Role of protein interactions in defining HIV-1 viral capsid shape and stability: a coarse-grained analysis.
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Biophys J,
98,
18-26.
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Y.Han,
J.Ahn,
J.Concel,
I.J.Byeon,
A.M.Gronenborn,
J.Yang,
and
T.Polenova
(2010).
Solid-state NMR studies of HIV-1 capsid protein assemblies.
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J Am Chem Soc,
132,
1976-1987.
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A.Alfadhli,
R.L.Barklis,
and
E.Barklis
(2009).
HIV-1 matrix organizes as a hexamer of trimers on membranes containing phosphatidylinositol-(4,5)-bisphosphate.
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Virology,
387,
466-472.
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A.M.Gronenborn
(2009).
Protein acrobatics in pairs--dimerization via domain swapping.
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Curr Opin Struct Biol,
19,
39-49.
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C.S.Adamson,
K.Salzwedel,
and
E.O.Freed
(2009).
Virus maturation as a new HIV-1 therapeutic target.
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Expert Opin Ther Targets,
13,
895-908.
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E.Barklis,
A.Alfadhli,
C.McQuaw,
S.Yalamuri,
A.Still,
R.L.Barklis,
B.Kukull,
and
C.S.López
(2009).
Characterization of the in vitro HIV-1 capsid assembly pathway.
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J Mol Biol,
387,
376-389.
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G.Cardone,
J.G.Purdy,
N.Cheng,
R.C.Craven,
and
A.C.Steven
(2009).
Visualization of a missing link in retrovirus capsid assembly.
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Nature,
457,
694-698.
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G.D.Bailey,
J.K.Hyun,
A.K.Mitra,
and
R.L.Kingston
(2009).
Proton-linked dimerization of a retroviral capsid protein initiates capsid assembly.
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Structure,
17,
737-748.
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PDB codes:
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I.B.Hogue,
A.Hoppe,
and
A.Ono
(2009).
Quantitative fluorescence resonance energy transfer microscopy analysis of the human immunodeficiency virus type 1 Gag-Gag interaction: relative contributions of the CA and NC domains and membrane binding.
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J Virol,
83,
7322-7336.
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I.J.Byeon,
X.Meng,
J.Jung,
G.Zhao,
R.Yang,
J.Ahn,
J.Shi,
J.Concel,
C.Aiken,
P.Zhang,
and
A.M.Gronenborn
(2009).
Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function.
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Cell,
139,
780-790.
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PDB code:
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J.A.Briggs,
J.D.Riches,
B.Glass,
V.Bartonova,
G.Zanetti,
and
H.G.Kräusslich
(2009).
Structure and assembly of immature HIV.
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Proc Natl Acad Sci U S A,
106,
11090-11095.
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J.G.Purdy,
J.M.Flanagan,
I.J.Ropson,
and
R.C.Craven
(2009).
Retroviral capsid assembly: a role for the CA dimer in initiation.
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J Mol Biol,
389,
438-451.
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J.L.Neira
(2009).
The capsid protein of human immunodeficiency virus: designing inhibitors of capsid assembly.
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FEBS J,
276,
6110-6117.
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M.G.Mateu
(2009).
The capsid protein of human immunodeficiency virus: intersubunit interactions during virus assembly.
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FEBS J,
276,
6098-6109.
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O.Pornillos,
B.K.Ganser-Pornillos,
B.N.Kelly,
Y.Hua,
F.G.Whitby,
C.D.Stout,
W.I.Sundquist,
C.P.Hill,
and
M.Yeager
(2009).
X-ray structures of the hexameric building block of the HIV capsid.
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Cell,
137,
1282-1292.
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PDB codes:
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R.B.Jones,
F.Y.Yue,
X.X.Gu,
D.V.Hunter,
S.Mujib,
G.Gyenes,
R.D.Mason,
R.Mohamed,
K.S.MacDonald,
C.Kovacs,
and
M.A.Ostrowski
(2009).
Human immunodeficiency virus type 1 escapes from interleukin-2-producing CD4+ T-cell responses without high-frequency fixation of mutations.
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J Virol,
83,
8722-8732.
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S.Abdurahman,
A.Végvári,
M.Levi,
S.Höglund,
M.Högberg,
W.Tong,
I.Romero,
J.Balzarini,
and
A.Vahlne
(2009).
Isolation and characterization of a small antiretroviral molecule affecting HIV-1 capsid morphology.
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Retrovirology,
6,
34.
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S.Matsuoka,
E.Dam,
D.Lecossier,
F.Clavel,
and
A.J.Hance
(2009).
Modulation of HIV-1 infectivity and cyclophilin A-dependence by Gag sequence and target cell type.
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Retrovirology,
6,
21.
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X.Yu,
Q.Wang,
J.C.Yang,
I.Buch,
C.J.Tsai,
B.Ma,
S.Z.Cheng,
R.Nussinov,
and
J.Zheng
(2009).
Mutational analysis and allosteric effects in the HIV-1 capsid protein carboxyl-terminal dimerization domain.
|
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Biomacromolecules,
10,
390-399.
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Y.Kitagawa,
M.Maeda-Sato,
K.Tanaka,
M.Tobiume,
H.Sawa,
H.Hasegawa,
A.Kojima,
W.W.Hall,
T.Kurata,
T.Sata,
and
H.Takahashi
(2009).
Covalent bonded Gag multimers in human immunodeficiency virus type-1 particles.
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| |
Microbiol Immunol,
53,
609-620.
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|
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Y.Yan,
A.Buckler-White,
K.Wollenberg,
and
C.A.Kozak
(2009).
Origin, antiviral function and evidence for positive selection of the gammaretrovirus restriction gene Fv1 in the genus Mus.
|
| |
Proc Natl Acad Sci U S A,
106,
3259-3263.
|
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|
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B.K.Ganser-Pornillos,
M.Yeager,
and
W.I.Sundquist
(2008).
The structural biology of HIV assembly.
|
| |
Curr Opin Struct Biol,
18,
203-217.
|
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|
|
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|
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H.Zhang,
Q.Zhao,
S.Bhattacharya,
A.A.Waheed,
X.Tong,
A.Hong,
S.Heck,
F.Curreli,
M.Goger,
D.Cowburn,
E.O.Freed,
and
A.K.Debnath
(2008).
A cell-penetrating helical peptide as a potential HIV-1 inhibitor.
|
| |
J Mol Biol,
378,
565-580.
|
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J.G.Purdy,
J.M.Flanagan,
I.J.Ropson,
K.E.Rennoll-Bankert,
and
R.C.Craven
(2008).
Critical role of conserved hydrophobic residues within the major homology region in mature retroviral capsid assembly.
|
| |
J Virol,
82,
5951-5961.
|
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J.M.Phillips,
P.S.Murray,
D.Murray,
and
V.M.Vogt
(2008).
A molecular switch required for retrovirus assembly participates in the hexagonal immature lattice.
|
| |
EMBO J,
27,
1411-1420.
|
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L.A.Alcaraz,
M.Del Alamo,
M.G.Mateu,
and
J.L.Neira
(2008).
Structural mobility of the monomeric C-terminal domain of the HIV-1 capsid protein.
|
| |
FEBS J,
275,
3299-3311.
|
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P.M.Lokhandwala,
T.L.Nguyen,
J.B.Bowzard,
and
R.C.Craven
(2008).
Cooperative role of the MHR and the CA dimerization helix in the maturation of the functional retrovirus capsid.
|
| |
Virology,
376,
191-198.
|
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P.W.Keller,
M.C.Johnson,
and
V.M.Vogt
(2008).
Mutations in the spacer peptide and adjoining sequences in Rous sarcoma virus Gag lead to tubular budding.
|
| |
J Virol,
82,
6788-6797.
|
|
|
|
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|
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S.Abdurahman,
A.Végvári,
M.Youssefi,
M.Levi,
S.Höglund,
E.Andersson,
P.Horal,
B.Svennerholm,
J.Balzarini,
and
A.Vahlne
(2008).
Activity of the small modified amino acid alpha-hydroxy glycineamide on in vitro and in vivo human immunodeficiency virus type 1 capsid assembly and infectivity.
|
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
|
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