9MIH | pdb_00009mih

273-4D01 Fab in complex with HIV-1 BG505 SOSIP Env trimer and RM20A3 Fab

PDB DOI: https://doi.org/10.2210/pdb9MIH/pdb
EM Map EMD-48290: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Homo sapiens, Human immunodeficiency virus 1, Macaca mulatta
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2024-12-12 Released: 2025-05-21
Deposition Author(s): Phulera, S., Ozorowski, G., Ward, A.B.
Funding Organization(s): Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Precise targeting of HIV broadly neutralizing antibody precursors in humans

Caniels, T.G., Prabhakaran, M., Ozorowski, G., MacPhee, K.J., Wu, W., van der Straten, K., Agrawal, S., Derking, R., Reiss, E.I.M.M., Millard, K., Turroja, M., Desrosiers, A., Bethony, J., Malkin, E., Liesdek, M.H., van der Veen, A., Klouwens, M., Phulera, S., Wilson, I.A., Ward, A.B.

(2025) Science

DOI: https://doi.org/10.1126/science.adv5572

Macromolecule Content

Total Structure Weight: 344.85 kDa
Atom Count: 20,955
Modeled Residue Count: 2,577
Deposited Residue Count: 2,989
Unique protein chains: 6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
273-4D01 kappa chain Fv	A [auth L]	103	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120	B [auth A], F [auth C], J [auth E]	516	Human immunodeficiency virus 1	Mutation(s): 2 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: 16	Glycosylation Focus chain B [auth A] Focus chain F [auth C] Focus chain J [auth E]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	C [auth B], G [auth D], K [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: 1	Glycosylation Focus chain C [auth B] Focus chain G [auth D] Focus chain K [auth F]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RM20A3 heavy chain Fv	D [auth G], H [auth J], L [auth M]	125	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RM20A3 light chain Fv	E [auth I], I [auth K], M [auth N]	128	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
273-4D01 heavy chain Fv	N [auth H]	120	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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	O, P, Q, S, T	2		N-Glycosylation	Interactions Focus chain O Focus chain P Focus chain Q Focus chain S Focus chain T Interactions & Density Focus chain O Focus chain P Focus chain Q Focus chain S Focus chain T

Entity ID: 8
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	R	3		N-Glycosylation	Interactions Focus chain R Interactions & Density Focus chain R

Entity ID: 9
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	U	4		N-Glycosylation	Interactions Focus chain U Interactions & Density Focus chain U

Entity ID: 10
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	V	5		N-Glycosylation	Interactions Focus chain V Interactions & Density Focus chain V

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 BA [auth A] SDF format, chain BB [auth E] SDF format, chain DA [auth A] SDF format, chain DB [auth E] SDF format, chain EA [auth A] SDF format, chain EB [auth E] SDF format, chain FB [auth E] SDF format, chain GB [auth E] SDF format, chain HA [auth B] SDF format, chain HB [auth E] SDF format, chain IB [auth E] SDF format, chain JA [auth C] SDF format, chain JB [auth E] SDF format, chain KA [auth C] SDF format, chain KB [auth E] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain MB [auth F] SDF format, chain NA [auth C] SDF format, chain NB [auth F] SDF format, chain PA [auth C] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain UA [auth C] SDF format, chain X [auth A] SDF format, chain XA [auth D] SDF format, chain YA [auth D] SDF format, chain AA [auth A] SDF format, chain AB [auth E] SDF format, chain CA [auth A] SDF format, chain CB [auth E] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain IA [auth C] SDF format, chain LB [auth F] SDF format, chain OA [auth C] SDF format, chain QA [auth C] SDF format, chain TA [auth C] SDF format, chain VA [auth C] SDF format, chain W [auth A] SDF format, chain WA [auth C] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain ZA [auth E] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth E] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth E] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth E] MOL2 format, chain FB [auth E] MOL2 format, chain GB [auth E] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth E] MOL2 format, chain IB [auth E] MOL2 format, chain JA [auth C] MOL2 format, chain JB [auth E] MOL2 format, chain KA [auth C] MOL2 format, chain KB [auth E] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain MB [auth F] MOL2 format, chain NA [auth C] MOL2 format, chain NB [auth F] MOL2 format, chain PA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth D] MOL2 format, chain YA [auth D] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth E] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth E] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain LB [auth F] MOL2 format, chain OA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth E] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth E] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth E] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth E] mmCIF format, chain FB [auth E] mmCIF format, chain GB [auth E] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth E] mmCIF format, chain IB [auth E] mmCIF format, chain JA [auth C] mmCIF format, chain JB [auth E] mmCIF format, chain KA [auth C] mmCIF format, chain KB [auth E] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain MB [auth F] mmCIF format, chain NA [auth C] mmCIF format, chain NB [auth F] mmCIF format, chain PA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth D] mmCIF format, chain YA [auth D] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth E] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth E] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain LB [auth F] mmCIF format, chain OA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth E]	AA [auth A] AB [auth E] BA [auth A] BB [auth E] CA [auth A] AA [auth A], AB [auth E], BA [auth A], BB [auth E], CA [auth A], CB [auth E], DA [auth A], DB [auth E], EA [auth A], EB [auth E], FA [auth A], FB [auth E], GA [auth A], GB [auth E], HA [auth B], HB [auth E], IA [auth C], IB [auth E], JA [auth C], JB [auth E], KA [auth C], KB [auth E], LA [auth C], LB [auth F], MA [auth C], MB [auth F], NA [auth C], NB [auth F], OA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C], UA [auth C], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth D], Y [auth A], YA [auth D], Z [auth A], ZA [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth E] Focus chain BA [auth A] Focus chain BB [auth E] Focus chain CA [auth A] Focus chain CB [auth E] Focus chain DA [auth A] Focus chain DB [auth E] Focus chain EA [auth A] Focus chain EB [auth E] Focus chain FA [auth A] Focus chain FB [auth E] Focus chain GA [auth A] Focus chain GB [auth E] Focus chain HA [auth B] Focus chain HB [auth E] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain JA [auth C] Focus chain JB [auth E] Focus chain KA [auth C] Focus chain KB [auth E] Focus chain LA [auth C] Focus chain LB [auth F] Focus chain MA [auth C] Focus chain MB [auth F] Focus chain NA [auth C] Focus chain NB [auth F] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth D] Focus chain Y [auth A] Focus chain YA [auth D] Focus chain Z [auth A] Focus chain ZA [auth E] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth E] Focus chain BA [auth A] Focus chain BB [auth E] Focus chain CA [auth A] Focus chain CB [auth E] Focus chain DA [auth A] Focus chain DB [auth E] Focus chain EA [auth A] Focus chain EB [auth E] Focus chain FA [auth A] Focus chain FB [auth E] Focus chain GA [auth A] Focus chain GB [auth E] Focus chain HA [auth B] Focus chain HB [auth E] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain JA [auth C] Focus chain JB [auth E] Focus chain KA [auth C] Focus chain KB [auth E] Focus chain LA [auth C] Focus chain LB [auth F] Focus chain MA [auth C] Focus chain MB [auth F] Focus chain NA [auth C] Focus chain NB [auth F] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth D] Focus chain Y [auth A] Focus chain YA [auth D] Focus chain Z [auth A] Focus chain ZA [auth E]