9yqo

AMC008 v4.2 SOSIP Env trimer in complex with PGT121 and VRC01 Fabs

Method: ELECTRON MICROSCOPY D_max: 161.3 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Envelope glycoprotein gp41

Human immunodeficiency virus 1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 18 其他Polymer 45 PDB declaration: octadecameric（18） Consistent with protein copy count	Chain B； UniProt 1–154 Chain H； UniProt 1–154 Chain P； UniProt 1–154	Not recorded	VRC01 Fab heavy chain × 3 VRC01 Fab light chain × 3 PGT121 Fab light chain × 3 PGT121 Fab heavy chain × 3 HIV-1 envelope glycoprotein gp120 × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 33 ;alpha-D-mannopyranose-(1-2)-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 ; × 3 ;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 ; × 3 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 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 ; × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.26 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9YQO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9NBT AMC008 v4.2 SOSIP Env trimer in complex with VRC01 and 35O22 Fabs Deposited 2025-02-14	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain B 1–154（154 aa） Chain K 1–154（154 aa） Chain R 1–154（154 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.91 Å
9NBY AMC008 v4.2 SOSIP Env trimer in complex with PGT121, VRC01 and 3BC315 Fabs Deposited 2025-02-14	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: eicosameric	Chain B 1–154（154 aa） Chain D 1–154（154 aa） Chain F 1–154（154 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
9NC0 AMC008 v4.2 SOSIP Env trimer in complex with b12 Fab Deposited 2025-02-14	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 1–154（154 aa） Chain D 1–154（154 aa） Chain F 1–154（154 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.88 Å
9NC3 AMC008 v4.2 SOSIP Env trimer in complex with b12 and 3BC315 Fabs Deposited 2025-02-14	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain B 1–154（154 aa） Chain D 1–154（154 aa） Chain F 1–154（154 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.74 Å
9NC6 AMC008 v4.2 SOSIP Env trimer in complex with two 3BC315 Fabs Deposited 2025-02-14	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain B 1–154（154 aa） Chain D 1–154（154 aa） Chain F 1–154（154 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.52 Å
9NC8 AMC008 v4.2 SOSIP Env trimer in complex with one 3BC315 Fab Deposited 2025-02-14	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–154（154 aa） Chain D 1–154（154 aa） Chain F 1–154（154 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.55 Å
9OAJ AMC008 v4.2 SOSIP Env trimer in complex with CD4 D1D2 Deposited 2025-04-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric	Chain B 1–154（154 aa） Chain E 1–154（154 aa） Chain H 1–154（154 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.91 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q1AII4_HV1
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain B； PDBConstruct 1–154； UniProt 1–154 Author chain H； PDBConstruct 1–154； UniProt 1–154 Author chain P； PDBConstruct 1–154； UniProt 1–154

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9yqo
Deposition date deposition_date	2025-10-15
Structure title title	AMC008 v4.2 SOSIP Env trimer in complex with PGT121 and VRC01 Fabs
Keywords keywords	HIV-1 Envelope glycoprotein, broadly neutralizing antibodies, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	52.00 Å
Radius of gyration Rg (electron density) rg_electron	51.42 Å
Forward intensity I(0) i0	2123220000.00
Molecular weight molecular_weight	377010.0 kDa
Excluded volume excluded_volume	468470 Å³
Envelope volume envelope_volume	691120 Å³
Hydration-shell volume shell_volume	109220 Å³
Envelope diameter envelope_diameter	163.0 Å
Shell Rg shell_rg	56.90 Å
Envelope Rg envelope_rg	50.66 Å
Shape Rg shape_rg	51.44 Å
Total Rg total_rg	51.53 Å
Total atoms total_atoms	26433
Residues n_residues	3102
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	161.3 Å
Rg (real space) rg_real	51.78 Å
Rg uncertainty (real space) rg_real_error	1.06 Å
I(0) (real space) i0_real	2.1230e+09
I(0) uncertainty (real space) i0_real_error	4.1500e+07
Rg (reciprocal space) rg_reciprocal	52.17 Å
I(0) (reciprocal space) i0_reciprocal	2124000000.0000
Solution quality estimate total_estimate	0.8715
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	64.5 Å
Skewness Skewness skewness	0.128
Kurtosis Kurtosis kurtosis	-0.469
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	128700000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.585

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Description description	VRC01 Fab heavy chain
Molecular weight formula_weight	24395.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,C,I
Atom count atom_count	26433

QVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRGGAVNYARPLQGRVTMTRDVYSDTAFLELRSLTVDDTAVYFCTRGKNCDYNWDFEHWGRGTPVIVSSPSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	VRC01 Fab light chain
Molecular weight formula_weight	23172.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N,D,J

EIVLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGPDYNLTISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	PGT121 Fab light chain
Molecular weight formula_weight	22574.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q,E,K

SDISVAPGETARISCGEKSLGSRAVQWYQHRAGQAPSLIIYNNQDRPSGIPERFSGSPDSPFGTTATLTITSVEAGDEADYYCHIWDSRVPTKWVFGGGTTLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	PGT121 Fab heavy chain
Molecular weight formula_weight	25169.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R,F,L

QMQLQESGPGLVKPSETLSLTCSVSGASISDSYWSWIRRSPGKGLEWIGYVHKSGDTNYSPSLKSRVNLSLDTSKNQVSLSLVAATAADSGKYYCARTLHGRRIYGIVAFNEWFTYFYMDVWGNGTQVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	HIV-1 envelope glycoprotein gp120
Molecular weight formula_weight	55212.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,G,O

MDWTWILFLVAAATRVHSTEKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVRNVWATHACVPTDPSPQEVILENVTENFNMWTNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTNELKNTTKTNNSSWGGEMKNCSFNVTTSIRDKVQKEYALFYKLDIVPIDDDNNTSNYRLINCNTSVITQACPKITFEPIPIQFCTPAGFAILKCNNKKFNGKGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVIIRSDNFTDNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRWFYTTGEIIGDIRQAHCNLSRTQWNNTLKQIAIKLREQFENKTIVFNQSSGGDPEIVMHSFNCGGEFFYCNTTKLFNSTWNDTDIRGNNTEGNDTITIPCRIKQIVNMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGSESNTTEIFRPGGGDMRDNWRSELYKYKVVRIEPLGVAPTKCKRRVVQ

来源 Source

来源生物 organism	Human immunodeficiency virus 1
NCBI Class编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	Envelope glycoprotein gp41
Molecular weight formula_weight	17428.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,H,P

AVGTIGAMFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQNNLLRAPEAQQHLLQLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTSVPWNTSWSNKSLDKIWNNMTWMEWEREIDNYTSLIYTLLEESQNQQEKNEQELLELD

来源 Source

来源生物 organism	Human immunodeficiency virus 1
NCBI Class编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Homo sapiens

Entity 7 Entity 7 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	33

Entity 8 Entity 8 branched

Description description	;alpha-D-mannopyranose-(1-2)-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 ;
Molecular weight formula_weight	1073.0 kDa
Source method src_method	man
Copy count entity_count	3

Entity 9 Entity 9 branched

Description description	;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 ;
Molecular weight formula_weight	1559.4 kDa
Source method src_method	man
Copy count entity_count	3

Entity 10 Entity 10 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	3

Entity 11 Entity 11 branched

Description description	;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 ;
Molecular weight formula_weight	1073.0 kDa
Source method src_method	man
Copy count entity_count	3

Entity 12 Entity 12 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	18

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8. Citations (1)

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Resolution resolution	3.26 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	56692

fit	/app/data/saxs_computation/yq/9yqo/9yqo.fit
pddf	/app/data/pr_computation/yq/9yqo/9yqo.pr.out
profile	/app/data/saxs_computation/yq/9yqo/9yqo.dat

AMC008 v4.2 SOSIP Env trimer in complex with PGT121 and VRC01 Fabs

1. Protein Identity and Related Structures Protein Identity & Related Structures

Envelope glycoprotein gp41

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 polymer

Polymer Polymer

来源 Source

Entity 7 Entity 7 branched

Entity 8 Entity 8 branched

Entity 9 Entity 9 branched

Entity 10 Entity 10 branched

Entity 11 Entity 11 branched

Entity 12 Entity 12 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)