6VY2

Cryo-EM structure of M1214_N1 Fab in complex with CH505 TF chimeric SOSIP.664 Env trimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

VSV-Displayed HIV-1 Envelope Identifies Broadly Neutralizing Antibodies Class-Switched to IgG and IgA.

Jia, M.Liberatore, R.A.Guo, Y.Chan, K.W.Pan, R.Lu, H.Waltari, E.Mittler, E.Chandran, K.Finzi, A.Kaufmann, D.E.Seaman, M.S.Ho, D.D.Shapiro, L.Sheng, Z.Kong, X.P.Bieniasz, P.D.Wu, X.

(2020) Cell Host Microbe 27: 963

  • DOI: https://doi.org/10.1016/j.chom.2020.03.024
  • Primary Citation of Related Structures:  
    6VU2, 6VY2

  • PubMed Abstract: 

    The HIV-1 envelope (Env) undergoes conformational changes during infection. Broadly neutralizing antibodies (bNAbs) are typically isolated by using soluble Env trimers, which do not capture all Env states. To address these limitations, we devised a vesicular stomatitis virus (VSV)-based probe to display membrane-embedded Env trimers and isolated five bNAbs from two chronically infected donors, M4008 and M1214. Donor B cell receptor (BCR) repertoires identified two bNAb lineages, M4008_N1 and M1214_N1, that class-switched to immunoglobulin G (IgG) and IgA. Variants of these bNAbs reconstituted as IgA demonstrated broadly neutralizing activity, and the IgA fraction of M1214 plasma conferred neutralization. M4008_N1 epitope mapping revealed a glycan-independent V3 epitope conferring tier 2 virus neutralization. A 4.86-Å-resolution cryogenic electron microscopy (cryo-EM) structure of M1214_N1 complexed with CH505 SOSIP revealed another elongated epitope, the V2V5 corridor, extending from V2 to V5. Overall, the VSV ENV probe identified bNAb lineages with neutralizing IgG and IgA members targeting distinct sites of HIV-1 Env vulnerability.


  • Organizational Affiliation

    Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY 10016, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoprotein 120
A, C, E
487Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for A0A0A7I3C6 (Human immunodeficiency virus 1)
Explore A0A0A7I3C6 
Go to UniProtKB:  A0A0A7I3C6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A7I3C6
Glycosylation
Glycosylation Sites: 21
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoprotein 41
B, D, F
160Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus 1)
Explore Q2N0S5 
Go to UniProtKB:  Q2N0S5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S5
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
M1214 N1 Fab heavy chainG [auth H],
H [auth I],
I [auth J]
226Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
M1214 N1 Fab light chainJ [auth L],
K [auth M],
L [auth N]
214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-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-glucopyranoseGA [auth g],
Q,
WA [auth w]
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G94626GC
GlyCosmos:  G94626GC
GlyGen:  G94626GC
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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-glucopyranoseIA [auth i],
S,
YA [auth y]
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
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-glucopyranoseJA [auth j],
T,
ZA [auth z]
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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-glucopyranoseEB [auth 4],
OA [auth o],
Y
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G84881ST
GlyCosmos:  G84881ST
GlyGen:  G84881ST
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AC [auth E]
BC [auth E]
CC [auth E]
DC [auth F]
EC [auth F]
AC [auth E],
BC [auth E],
CC [auth E],
DC [auth F],
EC [auth F],
FC [auth F],
IB [auth A],
JB [auth A],
KB [auth A],
LB [auth A],
MB [auth A],
NB [auth B],
OB [auth B],
PB [auth B],
QB [auth C],
RB [auth C],
SB [auth C],
TB [auth C],
UB [auth C],
VB [auth D],
WB [auth D],
XB [auth D],
YB [auth E],
ZB [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17.1
RECONSTRUCTIONcryoSPARC2.14.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI122953
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI100151
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI145655

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-06-24
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-11-13
    Changes: Data collection, Database references, Refinement description, Structure summary