2QAD | pdb_00002qad

Structure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4

PDB DOI: https://doi.org/10.2210/pdb2QAD/pdb

Classification: viral protein/immune system
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens, Escherichia coli, human gammaherpesvirus 4
Mutation(s): No

Deposited: 2007-06-14 Released: 2007-09-25
Deposition Author(s): Huang, C.-C., Tang, M., Robinson, J., Wyatt, R., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.269 (Depositor), 0.208 (DCC)
R-Value Work:
0.202 (Depositor), 0.206 (DCC)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.9 of the entry. See complete history.

Literature

Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4

Huang, C.-C., Lam, S.N., Acharya, P., Tang, M., Xiang, S.-H., Hussan, S.S., Stanfield, R.L., Robinson, J., Sodroski, J., Wilson, I.A., Wyatt, R., Bewley, C.A., Kwong, P.D.

(2007) Science 317: 1930-1934

PubMed: 17901336 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1145373
Primary Citation Related Structures:
2QAD, 2RLL

PubMed 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.

Organizational Affiliation

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecule Content

Total Structure Weight: 216.74 kDa
Atom Count: 14,987
Modeled Residue Count: 1,876
Deposited Residue Count: 1,896
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A, E	322	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for P35961 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2)) Explore P35961 Go to UniProtKB: P35961
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35961
Glycosylation
Glycosylation Sites: 15	Glycosylation Focus chain A Focus chain E
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD4	B, F	181	Homo sapiens	Mutation(s): 0 Gene Names: CD4
UniProt & NIH Common Fund Data Resources
Find proteins for P01730 (Homo sapiens) Explore P01730 Go to UniProtKB: P01730
PHAROS: P01730 GTEx: ENSG00000010610
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01730
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-HIV-1 antibody 412d light chain	C, G	214	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-HIV-1 antibody 412d heavy chain	D, H	231	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857 Go to UniProtKB: P01857
PHAROS: P01857 GTEx: ENSG00000211896
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01857
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain SA [auth E] SDF format, chain S [auth A] SDF format, chain RA [auth E] SDF format, chain R [auth A] SDF format, chain QA [auth E] SDF format, chain Q [auth A] SDF format, chain PA [auth E] SDF format, chain P [auth A] SDF format, chain OA [auth E] SDF format, chain O [auth A] SDF format, chain NA [auth E] SDF format, chain N [auth A] SDF format, chain MA [auth E] SDF format, chain M [auth A] SDF format, chain LA [auth E] SDF format, chain L [auth A] SDF format, chain KA [auth E] SDF format, chain K [auth A] SDF format, chain JA [auth E] SDF format, chain J [auth A] SDF format, chain IA [auth E] SDF format, chain I [auth A] SDF format, chain HA [auth E] SDF format, chain GA [auth E] SDF format, chain FA [auth E] SDF format, chain EA [auth E] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth E] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain EA [auth E] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth E] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth E] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth E] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain EA [auth E]	EA [auth E] FA [auth E] GA [auth E] HA [auth E] I [auth A] EA [auth E], FA [auth E], GA [auth E], HA [auth E], I [auth A], IA [auth E], J [auth A], JA [auth E], K [auth A], KA [auth E], L [auth A], LA [auth E], M [auth A], MA [auth E], N [auth A], NA [auth E], O [auth A], OA [auth E], P [auth A], PA [auth E], Q [auth A], QA [auth E], R [auth A], RA [auth E], S [auth A], SA [auth E], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain R [auth A] Focus chain RA [auth E] Focus chain S [auth A] Focus chain SA [auth E] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain R [auth A] Focus chain RA [auth E] Focus chain S [auth A] Focus chain SA [auth E] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A]
MLA Query on MLA Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain XA [auth H] SDF format, chain VA [auth F] SDF format, chain AA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain XA [auth H] MOL2 format, chain VA [auth F] MOL2 format, chain AA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain XA [auth H] mmCIF format, chain VA [auth F] mmCIF format, chain AA [auth B]	AA [auth B], VA [auth F], XA [auth H], Y [auth A]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain VA [auth F] Focus chain XA [auth H] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth B] Focus chain VA [auth F] Focus chain XA [auth H] Focus chain Y [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain WA [auth F] SDF format, chain UA [auth E] SDF format, chain TA [auth E] SDF format, chain DA [auth D] SDF format, chain CA [auth C] SDF format, chain BA [auth C] MOL2 format, chain Z [auth A] MOL2 format, chain WA [auth F] MOL2 format, chain UA [auth E] MOL2 format, chain TA [auth E] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain Z [auth A] mmCIF format, chain WA [auth F] mmCIF format, chain UA [auth E] mmCIF format, chain TA [auth E] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C]	BA [auth C] CA [auth C] DA [auth D] TA [auth E] UA [auth E] BA [auth C], CA [auth C], DA [auth D], TA [auth E], UA [auth E], WA [auth F], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth D] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain WA [auth F] Focus chain Z [auth A] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth D] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain WA [auth F] Focus chain Z [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS Query on TYS	D, H	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.269 (Depositor), 0.208 (DCC)
R-Value Work: 0.202 (Depositor), 0.206 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.6	α = 90
b = 53.021	β = 104.64
c = 225.326	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
AMoRE	phasing
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-09-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-09-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2015-04-29
Changes: Non-polymer description
Version 1.3: 2017-08-16
Changes: Refinement description, Source and taxonomy
Version 1.4: 2017-10-18
Changes: Refinement description
Version 1.5: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.6: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary
Version 1.7: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.8: 2023-11-15
Changes: Data collection
Version 1.9: 2024-11-20
Changes: Structure summary