7T9B | pdb_00007t9b

ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs

PDB DOI: https://doi.org/10.2210/pdb7T9B/pdb
EM Map EMD-25755: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Macaca mulatta, Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2021-12-18 Released: 2022-09-28
Deposition Author(s): Berndsen, Z.T., Ward, A.B.
Funding Organization(s): Bill & Melinda Gates Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.72 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Priming HIV Envelope V2 Apex-directed broadly neutralizing antibody responses with protein or mRNA immunogens

Melzi, E., Willis, J., Ma, K., Lin, Y., Kratochvil, S., Berndsen, Z.T., Nair, U., Warner, J., Steichen, J., Pecetta, S., Perez, M., Kirsch, K., Ward, A.B., Schief, W., Batista, F.D.

(2022) Immunity

Macromolecule Content

Total Structure Weight: 339.57 kDa
Atom Count: 21,592
Modelled Residue Count: 2,595
Deposited Residue Count: 2,878
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Envelope ApexGT5 gp120	A, E [auth C], I [auth E]	473	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 17	Glycosylation Focus chain A Focus chain E [auth C] Focus chain I [auth E]
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Envelope ApexGT5 gp41	B, F [auth D], J [auth F]	153	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain B Focus chain F [auth D] Focus chain J [auth F]
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RM20A3 Fab Heavy Chain	C [auth J], G [auth M], K [auth O]	125	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RM20A3 Fab Light Chain	D [auth K], H [auth N], L [auth P]	128	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
GT5-d42.16 Fab Heavy Chain	M [auth H]	134	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
GT5-d42.16 Fab Light Chain	N [auth L]	107	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

Help

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c], DA [auth d], FA [auth f], GA [auth g], O [auth G], CA [auth c], DA [auth d], FA [auth f], GA [auth g], O [auth G], P [auth I], V, W, X, Z	2		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain DA [auth d] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain O [auth G] Focus chain P [auth I] Focus chain V Focus chain W Focus chain X Focus chain Z Interactions & Density Focus chain CA [auth c] Focus chain DA [auth d] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain O [auth G] Focus chain P [auth I] Focus chain V Focus chain W Focus chain X Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 8
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	EA [auth e], Q, Y	4		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain Q Focus chain Y Interactions & Density Focus chain EA [auth e] Focus chain Q Focus chain Y
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 9
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	HA [auth h], R	3		N-Glycosylation	Interactions Focus chain HA [auth h] Focus chain R Interactions & Density Focus chain HA [auth h] Focus chain R
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	S	7		N-Glycosylation	Interactions Focus chain S Interactions & Density Focus chain S

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], IA [auth i], T	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain IA [auth i] Focus chain T Interactions & Density Focus chain AA [auth a] Focus chain IA [auth i] Focus chain T
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 12
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], JA [auth j], U	3		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain JA [auth j] Focus chain U Interactions & Density Focus chain BA [auth b] Focus chain JA [auth j] Focus chain U
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain GB [auth C] SDF format, chain HB [auth C] SDF format, chain IB [auth C] SDF format, chain KA [auth A] SDF format, chain KB [auth D] SDF format, chain LA [auth A] SDF format, chain LB [auth D] SDF format, chain MA [auth A] SDF format, chain MB [auth E] SDF format, chain NA [auth A] SDF format, chain NB [auth E] SDF format, chain OA [auth A] SDF format, chain OB [auth E] SDF format, chain PA [auth A] SDF format, chain PB [auth E] SDF format, chain QB [auth E] SDF format, chain RB [auth E] SDF format, chain SA [auth A] SDF format, chain SB [auth E] SDF format, chain TA [auth A] SDF format, chain TB [auth E] SDF format, chain UA [auth A] SDF format, chain UB [auth E] SDF format, chain VA [auth A] SDF format, chain VB [auth E] SDF format, chain WA [auth B] SDF format, chain WB [auth E] SDF format, chain XA [auth B] SDF format, chain XB [auth F] SDF format, chain YA [auth C] SDF format, chain YB [auth F] SDF format, chain ZA [auth C] SDF format, chain AB [auth C] SDF format, chain JB [auth C] SDF format, chain QA [auth A] SDF format, chain RA [auth A] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth D] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth D] MOL2 format, chain MA [auth A] MOL2 format, chain MB [auth E] MOL2 format, chain NA [auth A] MOL2 format, chain NB [auth E] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth E] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth E] MOL2 format, chain QB [auth E] MOL2 format, chain RB [auth E] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth E] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth E] MOL2 format, chain UA [auth A] MOL2 format, chain UB [auth E] MOL2 format, chain VA [auth A] MOL2 format, chain VB [auth E] MOL2 format, chain WA [auth B] MOL2 format, chain WB [auth E] MOL2 format, chain XA [auth B] MOL2 format, chain XB [auth F] MOL2 format, chain YA [auth C] MOL2 format, chain YB [auth F] MOL2 format, chain ZA [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain JB [auth C] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] mmCIF format, chain BB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain IB [auth C] mmCIF format, chain KA [auth A] mmCIF format, chain KB [auth D] mmCIF format, chain LA [auth A] mmCIF format, chain LB [auth D] mmCIF format, chain MA [auth A] mmCIF format, chain MB [auth E] mmCIF format, chain NA [auth A] mmCIF format, chain NB [auth E] mmCIF format, chain OA [auth A] mmCIF format, chain OB [auth E] mmCIF format, chain PA [auth A] mmCIF format, chain PB [auth E] mmCIF format, chain QB [auth E] mmCIF format, chain RB [auth E] mmCIF format, chain SA [auth A] mmCIF format, chain SB [auth E] mmCIF format, chain TA [auth A] mmCIF format, chain TB [auth E] mmCIF format, chain UA [auth A] mmCIF format, chain UB [auth E] mmCIF format, chain VA [auth A] mmCIF format, chain VB [auth E] mmCIF format, chain WA [auth B] mmCIF format, chain WB [auth E] mmCIF format, chain XA [auth B] mmCIF format, chain XB [auth F] mmCIF format, chain YA [auth C] mmCIF format, chain YB [auth F] mmCIF format, chain ZA [auth C] mmCIF format, chain AB [auth C] mmCIF format, chain JB [auth C] mmCIF format, chain QA [auth A] mmCIF format, chain RA [auth A]	AB [auth C] BB [auth C] CB [auth C] DB [auth C] EB [auth C] AB [auth C], BB [auth C], CB [auth C], DB [auth C], EB [auth C], FB [auth C], GB [auth C], HB [auth C], IB [auth C], JB [auth C], KA [auth A], KB [auth D], LA [auth A], LB [auth D], MA [auth A], MB [auth E], NA [auth A], NB [auth E], OA [auth A], OB [auth E], PA [auth A], PB [auth E], QA [auth A], QB [auth E], RA [auth A], RB [auth E], SA [auth A], SB [auth E], TA [auth A], TB [auth E], UA [auth A], UB [auth E], VA [auth A], VB [auth E], WA [auth B], WB [auth E], XA [auth B], XB [auth F], YA [auth C], YB [auth F], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain KA [auth A] Focus chain KB [auth D] Focus chain LA [auth A] Focus chain LB [auth D] Focus chain MA [auth A] Focus chain MB [auth E] Focus chain NA [auth A] Focus chain NB [auth E] Focus chain OA [auth A] Focus chain OB [auth E] Focus chain PA [auth A] Focus chain PB [auth E] Focus chain QA [auth A] Focus chain QB [auth E] Focus chain RA [auth A] Focus chain RB [auth E] Focus chain SA [auth A] Focus chain SB [auth E] Focus chain TA [auth A] Focus chain TB [auth E] Focus chain UA [auth A] Focus chain UB [auth E] Focus chain VA [auth A] Focus chain VB [auth E] Focus chain WA [auth B] Focus chain WB [auth E] Focus chain XA [auth B] Focus chain XB [auth F] Focus chain YA [auth C] Focus chain YB [auth F] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain KA [auth A] Focus chain KB [auth D] Focus chain LA [auth A] Focus chain LB [auth D] Focus chain MA [auth A] Focus chain MB [auth E] Focus chain NA [auth A] Focus chain NB [auth E] Focus chain OA [auth A] Focus chain OB [auth E] Focus chain PA [auth A] Focus chain PB [auth E] Focus chain QA [auth A] Focus chain QB [auth E] Focus chain RA [auth A] Focus chain RB [auth E] Focus chain SA [auth A] Focus chain SB [auth E] Focus chain TA [auth A] Focus chain TB [auth E] Focus chain UA [auth A] Focus chain UB [auth E] Focus chain VA [auth A] Focus chain VB [auth E] Focus chain WA [auth B] Focus chain WB [auth E] Focus chain XA [auth B] Focus chain XB [auth F] Focus chain YA [auth C] Focus chain YB [auth F] Focus chain ZA [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS Query on TYS	M [auth H]	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S		TYR

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.72 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-09-28

Deposition Author(s):

Berndsen, Z.T.

Ward, A.B.

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1084519
Bill & Melinda Gates Foundation	United States	OPP1196345
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 Al100663
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI144462