6N1W

Cryo-EM structure at 4.2 A resolution of vaccine-elicited antibody DFPH-a.15 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122

• PDB DOI: https://doi.org/10.2210/pdb6N1W/pdb
• EM Map EMD-9320: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1, Macaca mulatta, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2018-11-12 Released: 2019-07-24 
• Deposition Author(s): Acharya, P., Kwong, P.D.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 24-mer - A3B3C3D3E3F3G3H3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 24-mer - A16B3C3D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 534.63 kDa 
• Atom Count: 31,905 
• Modelled Residue Count: 3,852 
• Deposited Residue Count: 4,587 
• Unique protein chains: 8

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	A [auth 2], I [auth C], Q [auth c]	473	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6  Go to UniProtKB:  Q2N0S6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DFPH-a.15 heavy chain	B [auth 3], K [auth H], S [auth h]	224	Macaca mulatta	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DFPH-a.15 Light chain	C [auth 4], L, T [auth l]	212	Macaca mulatta	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT122 Heavy chain	D [auth 5], M, U [auth m]	132	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT122 Light chain	E [auth 6], N, V [auth n]	105	Homo sapiens	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC03 Light chain	F [auth 7], P [auth R], X [auth r]	102	Homo sapiens	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC03 Heavy chain	G [auth 8], O [auth Q], W [auth q]	128	Homo sapiens	Mutation(s): 0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	H [auth A], J [auth D], R [auth d]	153	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
UniProt
Find proteins for Q2N0S7 (Human immunodeficiency virus 1) Explore Q2N0S7  Go to UniProtKB:  Q2N0S7

Oligosaccharides

Help

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth F], AB [auth t], BA [auth G], BB [auth u], CA [auth I], CB [auth v], EA [auth K], EB [auth x], FA [auth O], FB [auth y], JA [auth U], JB [auth 9], LA [auth W], NA [auth Y], OA [auth Z], PA [auth a], RA [auth e], SA [auth f], WA [auth k], Y [auth B], YA [auth p]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranose	HA [auth S], HB [auth 0], KA [auth V], KB [auth AA], MA [auth X], UA [auth i], XA [auth o], Z [auth E], ZA [auth s]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

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	DA [auth J], DB [auth w], QA [auth b]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 12
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	GA [auth P], GB [auth z], TA [auth g]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

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-(1-3)-[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-glucopyranose	IA [auth T], IB [auth 1], VA [auth j]	9		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G68668TB GlyCosmos:  G68668TB GlyGen:  G68668TB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	LB [auth 2], MB [auth 2], NB [auth 2], OB [auth C], PB [auth C], QB [auth C], RB [auth c], SB [auth c], TB [auth c]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-24 
Deposition Author(s): Acharya, P., Kwong, P.D.

Revision History  

• Version 1.0: 2019-07-24
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary