4NCO

Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with the Broadly Neutralizing Fab PGT122


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.70 Å
  • R-Value Free: 0.389 
  • R-Value Work: 0.375 
  • R-Value Observed: 0.376 

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This is version 2.0 of the entry. See complete history


Literature

Crystal structure of a soluble cleaved HIV-1 envelope trimer.

Julien, J.P.Cupo, A.Sok, D.Stanfield, R.L.Lyumkis, D.Deller, M.C.Klasse, P.J.Burton, D.R.Sanders, R.W.Moore, J.P.Ward, A.B.Wilson, I.A.

(2013) Science 342: 1477-1483

  • DOI: 10.1126/science.1245625
  • Primary Citation of Related Structures:  
    4NCO

  • PubMed Abstract: 
  • HIV-1 entry into CD4(+) target cells is mediated by cleaved envelope glycoprotein (Env) trimers that have been challenging to characterize structurally. Here, we describe the crystal structure at 4.7 angstroms of a soluble, cleaved Env trimer that is stabilized and antigenically near-native (termed the BG505 SOSIP ...

    HIV-1 entry into CD4(+) target cells is mediated by cleaved envelope glycoprotein (Env) trimers that have been challenging to characterize structurally. Here, we describe the crystal structure at 4.7 angstroms of a soluble, cleaved Env trimer that is stabilized and antigenically near-native (termed the BG505 SOSIP.664 gp140 trimer) in complex with a potent broadly neutralizing antibody, PGT122. The structure shows a prefusion state of gp41, the interaction between the component gp120 and gp41 subunits, and how a close association between the gp120 V1/V2/V3 loops stabilizes the trimer apex around the threefold axis. The complete epitope of PGT122 on the trimer involves gp120 V1, V3, and several surrounding glycans. This trimer structure advances our understanding of how Env functions and is presented to the immune system, and provides a blueprint for structure-based vaccine design.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BG505 SOSIP gp120A, E, I475Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BG505 SOSIP gp41B, F, J78Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PGT122 light chainC, G, K211Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PGT122 heavy chainD, H, L235Homo sapiensMutation(s): 0 
Entity Groups  
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
BA [auth b],
M,
N,
O,
AA [auth a],
BA [auth b],
M,
N,
O,
P,
S,
T,
U,
V,
Y,
Z
7N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G55220VL
GlyCosmos:  G55220VL
GlyGen:  G55220VL
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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-glucopyranoseCA [auth c],
Q,
W
9N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G04216GB
GlyCosmos:  G04216GB
GlyGen:  G04216GB
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranoseDA [auth d],
R,
X
2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G53402KW
GlyCosmos:  G53402KW
GlyGen:  G53402KW
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth I],
BB [auth I],
CB [auth I],
DB [auth I],
EA [auth A],
AB [auth I],
BB [auth I],
CB [auth I],
DB [auth I],
EA [auth A],
EB [auth I],
FA [auth A],
FB [auth I],
GA [auth A],
GB [auth I],
HA [auth A],
HB [auth I],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth E],
PA [auth E],
QA [auth E],
RA [auth E],
SA [auth E],
TA [auth E],
UA [auth E],
VA [auth E],
WA [auth E],
XA [auth E],
YA [auth I],
ZA [auth I]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 7
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900111
Query on PRD_900111
DA [auth R], R [auth X], X [auth d]2alpha-alpha-mannobioseOligosaccharide / Metabolism Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.70 Å
  • R-Value Free: 0.389 
  • R-Value Work: 0.375 
  • R-Value Observed: 0.376 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.2α = 90
b = 260.72β = 99.56
c = 283.18γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2014-01-15
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary