4JAM

Crystal structure of broadly neutralizing anti-hiv-1 antibody ch103

PDB DOI: https://doi.org/10.2210/pdb4JAM/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2013-02-18 Released: 2013-04-03
Deposition Author(s): Zhou, T., Moquin, S., Zheng, A., Srivatsan, S., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.197
R-Value Work: 0.169
R-Value Observed: 0.170

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus.

Liao, H.X., Lynch, R., Zhou, T., Gao, F., Alam, S.M., Boyd, S.D., Fire, A.Z., Roskin, K.M., Schramm, C.A., Zhang, Z., Zhu, J., Shapiro, L., Mullikin, J.C., Gnanakaran, S., Hraber, P., Wiehe, K., Kelsoe, G., Yang, G., Xia, S.M., Montefiori, D.C., Parks, R., Lloyd, K.E., Scearce, R.M., Soderberg, K.A., Cohen, M., Kamanga, G., Louder, M.K., Tran, L.M., Chen, Y., Cai, F., Chen, S., Moquin, S., Du, X., Joyce, M.G., Srivatsan, S., Zhang, B., Zheng, A., Shaw, G.M., Hahn, B.H., Kepler, T.B., Korber, B.T., Kwong, P.D., Mascola, J.R., Haynes, B.F.

(2013) Nature 496: 469-476

PubMed: 23552890 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/nature12053
Primary Citation of Related Structures:
4JAM, 4JAN

PubMed Abstract:
Current human immunodeficiency virus-1 (HIV-1) vaccines elicit strain-specific neutralizing antibodies. However, cross-reactive neutralizing antibodies arise in approximately 20% of HIV-1-infected individuals, and details of their generation could provide a blueprint for effective vaccination. Here we report the isolation, evolution and structure of a broadly neutralizing antibody from an African donor followed from the time of infection. The mature antibody, CH103, neutralized approximately 55% of HIV-1 isolates, and its co-crystal structure with the HIV-1 envelope protein gp120 revealed a new loop-based mechanism of CD4-binding-site recognition. Virus and antibody gene sequencing revealed concomitant virus evolution and antibody maturation. Notably, the unmutated common ancestor of the CH103 lineage avidly bound the transmitted/founder HIV-1 envelope glycoprotein, and evolution of antibody neutralization breadth was preceded by extensive viral diversification in and near the CH103 epitope. These data determine the viral and antibody evolution leading to induction of a lineage of HIV-1 broadly neutralizing antibodies, and provide insights into strategies to elicit similar antibodies by vaccination.

Organizational Affiliation

Duke University Human Vaccine Institute, Departments of Medicine and Immunology, Duke University School of Medicine, Durham, North Carolina 27710, USA. hliao@duke.edu

Macromolecule Content

Total Structure Weight: 95.24 kDa
Atom Count: 7,297
Modelled Residue Count: 853
Deposited Residue Count: 870
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN of CH103	A [auth H], C [auth A]	226	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN of CH103	B [auth L], D [auth B]	209	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain E [auth H] SDF format, chain EA [auth B] SDF format, chain F [auth H] SDF format, chain G [auth H] SDF format, chain H SDF format, chain I [auth H] SDF format, chain J [auth H] SDF format, chain Q [auth L] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth H] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain Q [auth L] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain E [auth H] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth H] mmCIF format, chain G [auth H] mmCIF format, chain H mmCIF format, chain I [auth H] mmCIF format, chain J [auth H] mmCIF format, chain Q [auth L] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] E [auth H] AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth H], EA [auth B], F [auth H], G [auth H], H, I [auth H], J [auth H], Q [auth L], S [auth A], T [auth A], U [auth A], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth H] Focus chain EA [auth B] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain Q [auth L] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth H] Focus chain EA [auth B] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain Q [auth L] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain Z [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain P [auth H] MOL2 format, chain P [auth H] mmCIF format, chain P [auth H]	P [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth H] Interactions & Density Focus chain P [auth H]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain K [auth H] SDF format, chain L [auth H] SDF format, chain M [auth H] SDF format, chain N [auth H] SDF format, chain O [auth H] SDF format, chain R [auth L] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain M [auth H] MOL2 format, chain N [auth H] MOL2 format, chain O [auth H] MOL2 format, chain R [auth L] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain K [auth H] mmCIF format, chain L [auth H] mmCIF format, chain M [auth H] mmCIF format, chain N [auth H] mmCIF format, chain O [auth H] mmCIF format, chain R [auth L] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A]	FA [auth B] GA [auth B] K [auth H] L [auth H] M [auth H] FA [auth B], GA [auth B], K [auth H], L [auth H], M [auth H], N [auth H], O [auth H], R [auth L], V [auth A], W [auth A], X [auth A], Y [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain GA [auth B] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Focus chain O [auth H] Focus chain R [auth L] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain FA [auth B] Focus chain GA [auth B] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Focus chain O [auth H] Focus chain R [auth L] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.197
R-Value Work: 0.169
R-Value Observed: 0.170
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.027	α = 90
b = 146.375	β = 97.71
c = 66.322	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-04-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-04-03
Type: Initial release
Version 1.1: 2013-04-17
Changes: Database references
Version 1.2: 2013-05-01
Changes: Database references
Version 1.3: 2013-05-29
Changes: Database references
Version 1.4: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-11-27
Changes: Structure summary