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8d21

Cryo-EM structure of the VRC321 clinical trial, vaccine-elicited, human antibody 1B06 in complex with a stabilized NC99 HA trimer

Method: ELECTRON MICROSCOPY Dmax: 170.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Hemagglutinin HA2 chain

Influenza A virus

UniProt Q289M7

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 × 12 其他Polymer 3 PDB declaration: dodecameric（12） Consistent with protein copy count Chain B； UniProt 344–519 Chain C； UniProt 344–519 Chain G； UniProt 344–519 Not recorded Hemagglutinin HA1 chain × 3 （Q6WG00） 1B06 Heavy Chain × 3 1B06 Light Chain × 3 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 × 21 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；PBS cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.96 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 8D21 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7MFG Cryo-EM structure of the VRC310 clinical trial, vaccine-elicited, human antibody 310-030-1D06 Fab in complex with an H1 NC99 HA trimer Deposited 2021-04-09 Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 344–519（176 aa）
Chain D 344–519（176 aa）
Chain I 344–519（176 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.87 Å
7SCN Structure of H1 NC99 influenza hemagglutinin bound to Fab 310-63E6 Deposited 2021-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 18–339（322 aa）
Chain B 343–520（178 aa）
Chain C 18–339（322 aa）
Chain D 343–520（178 aa）
Chain G 18–339（322 aa）
Chain I 343–520（178 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；TBS buffer, PH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Blotting time: 5.5 s Blotting force: 0 Waiting time: 7 s
Resolution 3.02 Å
7SCO Structure of H1 influenza hemagglutinin bound to Fab 310-39G10 Deposited 2021-09-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 18–339（322 aa）
Chain B 343–520（178 aa）
Chain C 18–339（322 aa）
Chain D 343–520（178 aa）
Chain G 18–339（322 aa）
Chain I 343–520（178 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；TBS buffer, PH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Blotting time: 5.5 s Blotting force: 0 Waiting time: 7 s
Resolution 3.37 Å
8UR5 I53_dn5 nanoparticle displaying the trimeric HA heads with heptad domain, TH-1heptad-I53_dn5 (local refinement of TH-1heptad) Deposited 2023-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 64–280（217 aa）
Chain B 64–280（217 aa）
Chain C 64–280（217 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8UR7 I53_dn5 nanoparticle displaying the trimeric HA heads with heptad domain, TH-6heptad-I53_dn5 (local refinement of TH-6heptad) Deposited 2023-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 64–280（217 aa）
Chain B 64–280（217 aa）
Chain C 64–280（217 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HEMA_I00A1
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 1–176； UniProt 344–519 Author chain C； PDBConstruct 1–176； UniProt 344–519 Author chain G； PDBConstruct 1–176； UniProt 344–519

Hemagglutinin HA1 chain

Influenza A virus

UniProt Q6WG00

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 × 12 其他Polymer 3 PDB declaration: dodecameric（12） Consistent with protein copy count Chain A； UniProt 18–343 Chain D； UniProt 18–343 Chain I； UniProt 18–343 Not recorded Hemagglutinin HA2 chain × 3 （Q289M7） 1B06 Heavy Chain × 3 1B06 Light Chain × 3 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 × 21 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；PBS cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.96 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 8D21 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5C0R Crystal Structure of a Generation 3 Influenza Hemagglutinin Stabilized Stem Complexed with the Broadly Neutralizing Antibody C179 Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 18–49（32 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485
Chain A 328–402（75 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485
Chain A 436–517（82 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；15% (w/v) PEG 1500, 5% (v/v) MPD, 200 mM ammonium chloride, 100 mM Tris, pH 8.5
Resolution 3.19 Å R-free 0.251
5C0S Crystal structure of a generation 4 influenza hemagglutinin stabilized stem in complex with the broadly neutralizing antibody CR6261 Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 18–49（32 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485
Chain A 328–402（75 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485
Chain A 436–517（82 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；7% (w/v) PEG 4000, 4.5% (v/v) isopropanol, 100 mM imidazole, pH 6.5
Resolution 4.30 Å R-free 0.310
7MFG Cryo-EM structure of the VRC310 clinical trial, vaccine-elicited, human antibody 310-030-1D06 Fab in complex with an H1 NC99 HA trimer Deposited 2021-04-09 Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 18–343（326 aa）
Chain C 18–343（326 aa）
Chain G 18–343（326 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.87 Å
8TP3 H1 hemagglutinin (NC99) in complex with RBS-targeting Fab 1-1-1F05 Deposited 2023-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–343（343 aa）
Chain B 344–565（222 aa）
Chain C 1–343（343 aa）
Chain D 344–565（222 aa）
Chain G 1–343（343 aa）
Chain I 344–565（222 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TP5 H1 hemagglutinin (NC99) in complex with RBS-targeting Fab 1-1-1E04 Deposited 2023-08-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric
Chain A 18–339（322 aa）
Chain B 344–514（171 aa）
Chain C 18–339（322 aa）
Chain D 344–514（171 aa）
Chain G 18–339（322 aa）
Chain I 344–514（171 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8TPA H1 hemagglutinin (NC99) in complex with medial-junction-targeting Fab 2-2-1G06 Deposited 2023-08-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric
Chain A 1–343（343 aa）
Chain B 344–565（222 aa）
Chain C 1–343（343 aa）
Chain F 344–565（222 aa）
Chain G 1–343（343 aa）
Chain K 344–565（222 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9B2M Hemagglutinin H1 New Caledonia 1999 in complex with monoclonal antibody Fab 43_S0008 Deposited 2024-03-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–339（339 aa）
Chain B 340–565（226 aa）
Chain C 1–339（339 aa）
Chain D 340–565（226 aa）
Chain G 1–339（339 aa）
Chain I 340–565（226 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；TBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
9CJY CryoEM structure of NC99 hemagglutinin trimer in complex with Fab BB798E 3-C07 Deposited 2024-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain A 18–343（326 aa）
Chain B 344–519（176 aa）
Chain C 18–343（326 aa）
Chain D 344–519（176 aa）
Chain E 18–343（326 aa）
Chain F 344–519（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9CJZ CryoEM structure of NC99 hemagglutinin trimer in complex with Fab T009 3-E04 Deposited 2024-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain A 18–343（326 aa）
Chain B 344–519（176 aa）
Chain C 18–343（326 aa）
Chain D 344–519（176 aa）
Chain E 18–343（326 aa）
Chain F 344–519（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q6WG00_9INFA
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–326； UniProt 18–343 Author chain D； PDBConstruct 1–326； UniProt 18–343 Author chain I； PDBConstruct 1–326； UniProt 18–343

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

SAXS profile for 8d21

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8d21
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8d21
Deposition date deposition_date2022-05-27
Structure title titleCryo-EM structure of the VRC321 clinical trial, vaccine-elicited, human antibody 1B06 in complex with a stabilized NC99 HA trimer
Keywords keywordsVRC, IMMUNE SYSTEM, VRC321, Fab, Stem, IMMUNE SYSTEM-Viral Protein complex; IMMUNE SYSTEM/Viral Protein
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier50.92 Å
Radius of gyration Rg (electron density) rg_electron51.01 Å
Forward intensity I(0) i0933032000.00
Molecular weight molecular_weight249130.0 kDa
Excluded volume excluded_volume309450 ų
Envelope volume envelope_volume450620 ų
Hydration-shell volume shell_volume75217 ų
Envelope diameter envelope_diameter168.9 Å
Shell Rg shell_rg52.61 Å
Envelope Rg envelope_rg50.21 Å
Shape Rg shape_rg51.02 Å
Total Rg total_rg51.00 Å
Total atoms total_atoms17541
Residues n_residues2127
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax170.0 Å
Rg (real space) rg_real50.96 Å
Rg uncertainty (real space) rg_real_error1.45 Å
I(0) (real space) i0_real9.3300e+08
I(0) uncertainty (real space) i0_real_error1.6850e+07
Rg (reciprocal space) rg_reciprocal50.86 Å
I(0) (reciprocal space) i0_reciprocal932900000.0000
Solution quality estimate total_estimate0.8848
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.4 Å
Skewness Skewness skewness0.272
Kurtosis Kurtosis kurtosis-0.696
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha94160000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.877
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id8d21A01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily20 — Haemagglutinin, alpha/beta domain, HA1 chain
Domain ID domain_id8d21B01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10 —
Domain ID domain_id8d21C01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10 —
Domain ID domain_id8d21D01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily20 — Haemagglutinin, alpha/beta domain, HA1 chain
Domain ID domain_id8d21E01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8d21F01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8d21G01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10 —
Domain ID domain_id8d21H01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8d21I01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily20 — Haemagglutinin, alpha/beta domain, HA1 chain
Domain ID domain_id8d21J01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8d21K01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8d21L01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)