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* Residue conservation analysis
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PDB id:
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Viral protein
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Title:
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Molecular structure for the HIV-1 gp120 trimer in the unliganded state
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Structure:
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HIV-1 envelope glycoprotein gp120. Chain: a, d, g. Fragment: core: residues 90-124. Synonym: su, glycoprotein 120, gp120. Engineered: yes. HIV-1 envelope glycoprotein gp120. Chain: b, e, h. Fragment: core: residues 198-396. Synonym: su, glycoprotein 120, gp120.
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Source:
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HIV-1 m:b_hxb2r. Organism_taxid: 11706. Strain: isolate hxb2 group m subtype b, bal. Gene: env. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_taxid: 9606
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Authors:
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M.J.Borgnia,J.Liu,A.Bartesaghi,G.Sapiro,S.Subramaniam
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Key ref:
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J.Liu
et al.
(2008).
Molecular architecture of native HIV-1 gp120 trimers.
Nature,
455,
109-113.
PubMed id:
DOI:
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Date:
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02-Jul-08
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Release date:
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19-Aug-08
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PROCHECK
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Headers
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References
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P04578
(ENV_HV1H2) -
Envelope glycoprotein gp160 from Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)
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Seq:
Struc:
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856 a.a.
35 a.a.
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DOI no:
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Nature
455:109-113
(2008)
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PubMed id:
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Molecular architecture of native HIV-1 gp120 trimers.
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J.Liu,
A.Bartesaghi,
M.J.Borgnia,
G.Sapiro,
S.Subramaniam.
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ABSTRACT
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The envelope glycoproteins (Env) of human and simian immunodeficiency viruses
(HIV and SIV, respectively) mediate virus binding to the cell surface receptor
CD4 on target cells to initiate infection. Env is a heterodimer of a
transmembrane glycoprotein (gp41) and a surface glycoprotein (gp120), and forms
trimers on the surface of the viral membrane. Using cryo-electron tomography
combined with three-dimensional image classification and averaging, we report
the three-dimensional structures of trimeric Env displayed on native HIV-1 in
the unliganded state, in complex with the broadly neutralizing antibody b12 and
in a ternary complex with CD4 and the 17b antibody. By fitting the known crystal
structures of the monomeric gp120 core in the b12- and CD4/17b-bound
conformations into the density maps derived by electron tomography, we derive
molecular models for the native HIV-1 gp120 trimer in unliganded and CD4-bound
states. We demonstrate that CD4 binding results in a major reorganization of the
Env trimer, causing an outward rotation and displacement of each gp120 monomer.
This appears to be coupled with a rearrangement of the gp41 region along the
central axis of the trimer, leading to closer contact between the viral and
target cell membranes. Our findings elucidate the structure and conformational
changes of trimeric HIV-1 gp120 relevant to antibody neutralization and
attachment to target cells.
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Selected figure(s)
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Figure 1.
Figure 1: Averaged 3D structure of the HIV-1 spike in complex
with b12-Fab. a, Perspective view of the surface of the
density map shown at two thresholds; one to include the entire
spike (outer), and another to highlight the Fab and gp120
components (inner). b–d, Front (b, c) and top (d) views of the
map fitted with X-ray coordinates of the complex of the Fab
fragment of b12 (cyan) with gp120 (red, PDB ID, 2NY7); only
gp120 coordinates are shown in c, which is at the inner
threshold. Likely locations of the V1/V2 loop and gp41 regions
are indicated by asterisks in d and the white arrow in b,
respectively. The stumps of the V1/V2 and V3 loop regions are
shown in yellow and green, respectively.
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Figure 4.
Figure 4: Description of the conformational change in the gp120
trimer induced by CD4 binding. a–d, Model for the
conformational change from the unliganded (a, c) to the
CD4-bound state (b, d) shown as top (a, b) and front (c, d)
views. The gp120 core, CD4, V1/V2 and V3 stems are shown in
white, yellow, red and green colours, respectively. e, Schematic
description of the gp41 (blue) and gp120 (red/purple) regions of
the trimeric spike and the conformational changes that occur
upon CD4 binding. The yellow patch near the apex marks the
location of the CD4 binding site in the unliganded spike and the
green patch at the apex marks the location of the V3 loop region
in the spike after CD4 binding. f, Schematic view of the
consequence of the CD4-induced conformational changes for viral
attachment to the target cell and interaction with chemokine
receptors (green at top). Colours in f have same meaning as in e.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2008,
455,
109-113)
copyright 2008.
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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,
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A.Herschhorn,
S.H.Xiang,
H.Haim,
X.Yang,
and
J.Sodroski
(2012).
Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer.
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Nat Struct Mol Biol,
19,
893-899.
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B.Wei,
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and
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Use of mutual information arrays to predict coevolving sites in the full length HIV gp120 protein for subtypes B and C.
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Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.
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Nature,
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PDB codes:
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L.T.Da,
J.M.Quan,
and
Y.D.Wu
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Understanding the binding mode and function of BMS-488043 against HIV-1 viral entry.
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Proteins,
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M.Caffrey
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and
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B.Wu,
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PDB codes:
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C.Sundling,
S.O'Dell,
I.Douagi,
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J Virol,
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| |
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J Virol,
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PDB codes:
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J.M.Binley,
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Role of complex carbohydrates in human immunodeficiency virus type 1 infection and resistance to antibody neutralization.
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Human anti-HIV-neutralizing antibodies frequently target a conserved epitope essential for viral fitness.
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PDB code:
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K.J.Doores,
Z.Fulton,
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Antibody 2G12 recognizes di-mannose equivalently in domain- and nondomain-exchanged forms but only binds the HIV-1 glycan shield if domain exchanged.
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J Virol,
84,
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PDB code:
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K.Miyauchi,
A.R.Curran,
Y.Long,
N.Kondo,
A.Iwamoto,
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Retrovirology,
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J.A.Briggs,
H.G.Kräusslich,
and
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| |
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|
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107,
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PDB codes:
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PDB codes:
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R.Song,
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A V3 loop-dependent gp120 element disrupted by CD4 binding stabilizes the human immunodeficiency virus envelope glycoprotein trimer.
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J Virol,
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Proc Natl Acad Sci U S A,
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
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shown on the right.
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