6V6W | pdb_00006v6w

Crystal structure of antibody 438-B11 DSS mutant (Cys98A-100aA) in complex with an uncleaved prefusion optimized (UFO) soluble BG505 trimer and Fab 35O22

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.50 Å
  • R-Value Free: 
    0.355 (Depositor) 
  • R-Value Work: 
    0.309 (Depositor) 
  • R-Value Observed: 
    0.311 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Currently 6V6W does not have a validation slider image.


This is version 1.3 of the entry. See complete history. 


Literature

A VH1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite

Kumar, S., Ju, B., Shapero, B., Lin, X., Ren, L., Zhang, L., Li, D., Zhou, Z., Feng, Y., Sou, C., Mann, C.J., Hao, Y., Sarkar, A., Hou, J., Nunnally, C., Hong, K., Wang, S., Ge, X., Su, B., Landais, E., Sok, D., Zwick, M.B., He, L., Zhu, J., Wilson, I.A., Shao, Y.

(2020) Sci Adv 6: eabb1328


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
35O22 Fab Heavy chainA [auth D],
G [auth A]		243Human immunodeficiency virus 1Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
35O22 Fab Light chainB [auth E],
H [auth B]		216Human immunodeficiency virus 1Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120C [auth G],
I [auth C]		485Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 12
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
B11 DSS Fab heavy chainD [auth I],
J [auth F]		235Human immunodeficiency virus 1Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
B11 Fab light chainE [auth J],
K [auth H]		215Human immunodeficiency virus 1Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41F [auth T],
L [auth K]		140Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S9 (Human immunodeficiency virus type 1)
Explore Q2N0S9 
Go to UniProtKB:  Q2N0S9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S9
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth L],
P [auth O]		4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseN [auth M],
Q [auth P]		2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseO [auth N],
R [auth Q]		5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth T]
CA [auth T]
DA [auth T]
EA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.50 Å
  • R-Value Free:  0.355 (Depositor) 
  • R-Value Work:  0.309 (Depositor) 
  • R-Value Observed: 0.311 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.534α = 90
b = 148.534β = 90
c = 843.554γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-2000data scaling
HKL-2000data processing
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report

Currently 6V6W does not have a validation slider image.



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Derived calculations
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary