4LSQ | pdb_00004lsq

Crystal structure of broadly and potently neutralizing antibody VRC-CH31 in complex with HIV-1 clade A/E gp120 93TH057 with LOOP D and Loop V5 from clade A strain 3415_v1_c1

• PDB DOI: https://doi.org/10.2210/pdb4LSQ/pdb

• Classification: viral protein/immune system
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2013-07-23 Released: 2013-08-21 
• Deposition Author(s): Zhou, T., Moquin, S., Kwong, P.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.229 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway for HIV-1 Neutralization by VRC01-Class Antibodies.

Zhou, T., Zhu, J., Wu, X., Moquin, S., Zhang, B., Acharya, P., Georgiev, I.S., Altae-Tran, H.R., Chuang, G.Y., Joyce, M.G., Do Kwon, Y., Longo, N.S., Louder, M.K., Luongo, T., McKee, K., Schramm, C.A., Skinner, J., Yang, Y., Yang, Z., Zhang, Z., Zheng, A., Bonsignori, M., Haynes, B.F., Scheid, J.F., Nussenzweig, M.C., Simek, M., Burton, D.R., Koff, W.C., Mullikin, J.C., Connors, M., Shapiro, L., Nabel, G.J., Mascola, J.R., Kwong, P.D.

(2013) Immunity 39: 245-258

• PubMed: 23911655 
• DOI: https://doi.org/10.1016/j.immuni.2013.04.012
• Primary Citation Related Structures: 
  4LSP, 4LSQ, 4LSR, 4LSS, 4LST, 4LSU, 4LSV


• PubMed Abstract: 
  

  Antibodies of the VRC01 class neutralize HIV-1, arise in diverse HIV-1-infected donors, and are potential templates for an effective HIV-1 vaccine. However, the stochastic processes that generate repertoires in each individual of >10(12) antibodies make elicitation of specific antibodies uncertain. Here we determine the ontogeny of the VRC01 class by crystallography and next-generation sequencing. Despite antibody-sequence differences exceeding 50%, antibody-gp120 cocrystal structures reveal VRC01-class recognition to be remarkably similar. B cell transcripts indicate that VRC01-class antibodies require few specific genetic elements, suggesting that naive-B cells with VRC01-class features are generated regularly by recombination. Virtually all of these fail to mature, however, with only a few-likely one-ancestor B cell expanding to form a VRC01-class lineage in each donor. Developmental similarities in multiple donors thus reveal the generation of VRC01-class antibodies to be reproducible in principle, thereby providing a framework for attempts to elicit similar antibodies in the general population.

---

Organizational Affiliation: 
• Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.45 kDa 
• Atom Count: 6,515 
• Modeled Residue Count: 775 
• Deposited Residue Count: 798 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENVELOPE GLYCOPROTEIN GP120 WITH LOOP D AND V5 FROM STRAIN 3415_V1_C1	A [auth G]	352	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
UniProt
Find proteins for Q0ED31 (Human immunodeficiency virus type 1) Explore Q0ED31  Go to UniProtKB:  Q0ED31
Glycosylation
Glycosylation Sites: 9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAVY CHAIN OF ANTIBODY VRC-CH31	B [auth H]	236	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LIGHT CHAIN OF ANTIBODY VRC-CH31 WITH N70D MUTATION	C [auth L]	210	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth G], E [auth G], F [auth G], G, H [auth G], I [auth G], J [auth G], K [auth G], L [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CD	M [auth G], N [auth G], U [auth H], V [auth H], Y [auth L]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
BU3	O [auth G]	(R,R)-2,3-BUTANEDIOL C4 H10 O2 OWBTYPJTUOEWEK-QWWZWVQMSA-N
CL	P [auth G], W [auth H], X [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	Q [auth G], R [auth G], S [auth G], T [auth G]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.229 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.514	α = 90
b = 67.621	β = 90
c = 221.088	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-21 
Deposition Author(s): Zhou, T., Moquin, S., Kwong, P.D.

Revision History  

• Version 1.0: 2013-08-21
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references
• Version 1.2: 2013-09-25
  Changes: Database references
• Version 1.3: 2014-05-07
  Changes: Other
• Version 1.4: 2017-11-15
  Changes: Refinement description
• Version 1.5: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.6: 2024-11-06
  Changes: Data collection, Database references, Structure summary