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PDBsum entry 2qad
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Viral protein/immune system PDB id
2qad

 

 

 

 

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Contents
Protein chains
319 a.a. *
178 a.a. *
213 a.a. *
231 a.a. *
Ligands
NAG ×31
MLA ×4
EDO ×7
* Residue conservation analysis
PDB id:
2qad
Name: Viral protein/immune system
Title: Structure of tyrosine-sulfated 412d antibody complexed with HIV-1 yu2 gp120 and cd4
Structure: Envelope glycoprotein gp160. Chain: a, e. Fragment: core with v3. Synonym: env polyprotein. Engineered: yes. T-cell surface glycoprotein cd4. Chain: b, f. Fragment: d1d2, ig-like v-type and ig-like c2-type 1 domains. Synonym: t-cell surface antigen t4/leu-3.
Source: Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: yu2. Gene: env. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: embryonic cell line 293. Homo sapiens. Human.
Resolution:
3.30Å     R-factor:   0.202     R-free:   0.269
Authors: C.-C.Huang,M.Tang,J.Robinson,R.Wyatt,P.D.Kwong
Key ref:
C.C.Huang et al. (2007). Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4. Science, 317, 1930-1934. PubMed id: 17901336 DOI: 10.1126/science.1145373
Date:
14-Jun-07     Release date:   25-Sep-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P35961  (ENV_HV1Y2) -  Envelope glycoprotein gp160 from Human immunodeficiency virus type 1 group M subtype B (isolate YU-2)
Seq:
Struc: 		 
Seq:
Struc: 		843 a.a.
319 a.a.*
Protein chains
Pfam   ArchSchema ?
P01730  (CD4_HUMAN) -  T-cell surface glycoprotein CD4 from Homo sapiens
Seq:
Struc: 		458 a.a.
178 a.a.
Protein chains
No UniProt id for this chain
Struc: 213 a.a.
Protein chains
Pfam   ArchSchema ?
A4F255  (A4F255_HUMAN) -  Immunoblobulin G1 Fab heavy chain variable region (Fragment) from Homo sapiens
Seq:
Struc: 		234 a.a.
231 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 78 residue positions (black crosses)

 

 
DOI no: 10.1126/science.1145373 Science 317:1930-1934 (2007)
PubMed id: 17901336  
 
 
Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4.
C.C.Huang, S.N.Lam, P.Acharya, M.Tang, S.H.Xiang, S.S.Hussan, R.L.Stanfield, J.Robinson, J.Sodroski, I.A.Wilson, R.Wyatt, C.A.Bewley, P.D.Kwong.
 
  ABSTRACT  
 
The CCR5 co-receptor binds to the HIV-1 gp120 envelope glycoprotein and facilitates HIV-1 entry into cells. Its N terminus is tyrosine-sulfated, as are many antibodies that react with the co-receptor binding site on gp120. We applied nuclear magnetic resonance and crystallographic techniques to analyze the structure of the CCR5 N terminus and that of the tyrosine-sulfated antibody 412d in complex with gp120 and CD4. The conformations of tyrosine-sulfated regions of CCR5 (alpha-helix) and 412d (extended loop) are surprisingly different. Nonetheless, a critical sulfotyrosine on CCR5 and on 412d induces similar structural rearrangements in gp120. These results now provide a framework for understanding HIV-1 interactions with the CCR5 N terminus during viral entry and define a conserved site on gp120, whose recognition of sulfotyrosine engenders posttranslational mimicry by the immune system.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Structure of the tyrosine-sulfated antibody 412d in complex with HIV-1 gp120 and CD4. (A) Ribbon representation. CD4 is yellow, the heavy chain of Fab 412d is dark blue, the light chain is cyan, and gp120 is gray, except for the V3 loop, which is orange. The CDR H3 loop of 412d is red, with sulfotyrosines depicted in stick representation. (B) Close-up, with molecular surface of gp120 in gray and sulfotyrosines of 412d (red labels) and select residues of gp120 (black labels) in stick representation. Dotted lines represent coordinating hydrogen bonds between gp120 and the sulfate group of Tys100c^412d. The sulfate of Tys 100c^412d makes a full complement of ionic interactions: a salt bridge to Arg 298^gp120 and hydrogen bonds to the side-chain nitrogen of Asn 302^gp120, the side-chain hydroxyl of Thr 303^gp120, and the main-chain amides of 302^gp120, 303^gp120, and 441^gp120 (34). 		Figure 4.
Fig. 4. A conserved site for binding sulfotyrosine on HIV-1 gp120. (A) Alterations of the V3 base to accommodate binding of sulfotyrosine. The gp120 (gray) region around the V3 loop (orange) is illustrated in ribbon diagram, with an overlying semitransparent surface for unbound (left panel) and bound (right panel) conformations. Binding of the CCR5 N terminus (purple) or the 412d CDR H3 (red), each with two sulfotyrosines (stick representation, with red and purple labels), alters the V3 base, forming a sulfotyrosine binding pocket and a rigid ß-hairpin. (B) Close-up of the conserved sulfotyrosine binding pocket. The orientation shown is similar to that in Figs. 2B and 3B [ 90° from (A) about a diagonal axis, as defined by the long axis of the V3 from (A)]. Tys 14^CCR5 is shown in purple, with Tys 100c^412d in red. Select residues of gp120 are shown in stick representation and labeled in black. Hydrogen bonds coordinating the buried sulfate groups in each are depicted with dotted lines.
 
  The above figures are reprinted by permission from the AAAs: Science (2007, 317, 1930-1934) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

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PDB codes: 3ghb 3ghe
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PDB code: 3c2a
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Tyrosine-sulfate isosteres of CCR5 N-terminus as tools for studying HIV-1 entry.
  Bioorg Med Chem, 16, 10113-10120.  
18787705 S.Naganawa, M.Yokoyama, T.Shiino, T.Suzuki, Y.Ishigatsubo, A.Ueda, A.Shirai, M.Takeno, S.Hayakawa, S.Sato, O.Tochikubo, S.Kiyoura, K.Sawada, T.Ikegami, T.Kanda, K.Kitamura, and H.Sato (2008).
Net positive charge of HIV-1 CRF01_AE V3 sequence regulates viral sensitivity to humoral immunity.
  PLoS ONE, 3, e3206.  
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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