6NNJ
Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to CH31 scFv in Complex with Crystallization Chaperones 3H109L Fab and 35O22 scFv at 3.1 Angstrom
- PDB DOI: https://doi.org/10.2210/pdb6NNJ/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Human immunodeficiency virus 1, Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): Yes 
- Deposited: 2019-01-15 Released: 2019-02-27 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.293 
- R-Value Work: 0.248 
- R-Value Observed: 0.250 
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Envelope glycoprotein gp41 | A [auth B] | 153 | Human immunodeficiency virus 1 | Mutation(s): 2  Gene Names: env | |
UniProt | |||||
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6  Go to UniProtKB:  Q2N0S6 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q2N0S6 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
35O22 scFv heavy chain | B [auth D] | 153 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
35O22 scFv light chain | C [auth E] | 130 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Envelope glycoprotein gp120 | D [auth G] | 481 | Human immunodeficiency virus 1 | Mutation(s): 3  Gene Names: env | |
UniProt | |||||
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6  Go to UniProtKB:  Q2N0S6 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q2N0S6 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
3H109L Fab heavy chain | E [auth H] | 244 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
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Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
3H109L Fab light chain | F [auth L] | 217 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
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Entity ID: 7 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
CH31 scFv heavy chain | G [auth U] | 137 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 8 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
CH31 scFv light chain | H [auth V] | 117 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 9 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-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 | I [auth A] | 6 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G09724ZC GlyCosmos:  G09724ZC GlyGen:  G09724ZC |
Entity ID: 10 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | J [auth C], M [auth J], N [auth K], O [auth M], Q [auth O] | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 11 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D 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-glucopyranose | K [auth F] | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Entity ID: 12 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D 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-glucopyranose | L [auth I] | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC |
Entity ID: 13 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-glucopyranose | P [auth N] | 10 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G40702WU GlyCosmos:  G40702WU GlyGen:  G40702WU |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | R [auth B] S [auth B] T [auth G] U [auth G] V [auth G] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.293 
- R-Value Work: 0.248 
- R-Value Observed: 0.250 
- Space Group: P 63
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 132.15 | α = 90 |
b = 132.15 | β = 90 |
c = 315.95 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2019-02-27  Deposition Author(s): Lai, Y.-T., Kwong, P.D.
Revision History (Full details and data files)
- Version 1.0: 2019-02-27
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary