SAXSdb — 7scn

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

Hemagglutinin HA1 chain

Influenza A virus (strain A/New Zealand:South Canterbury/35/2000 H1N1)

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 18–339 Chain B； UniProt 343–520 Chain C； UniProt 18–339 Chain D； UniProt 343–520 Chain G； UniProt 18–339 Chain I； UniProt 343–520	Not recorded	310-63E6 Fab, Heavy Chain × 3 310-63E6 Fab, Light Chain × 3 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

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 7SCN	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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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
7SCO Structure of H1 influenza hemagglutinin bound to Fab 310-39G10 Deposited 2021-09-28	Different oligomeric state Different ligand/ion 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
8D21 Cryo-EM structure of the VRC321 clinical trial, vaccine-elicited, human antibody 1B06 in complex with a stabilized NC99 HA trimer Deposited 2022-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 344–519（176 aa） Chain C 344–519（176 aa） Chain G 344–519（176 aa）	Not recorded	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
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 mutation/modification 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 mutation/modification 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, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–322； UniProt 18–339 Author chain C； PDBConstruct 1–322； UniProt 18–339 Author chain G； PDBConstruct 1–322； UniProt 18–339 Author chain B； PDBConstruct 4–181； UniProt 343–520 Author chain D； PDBConstruct 4–181； UniProt 343–520 Author chain I； PDBConstruct 4–181； UniProt 343–520

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7scn
Deposition date deposition_date	2021-09-28
Structure title title	Structure of H1 NC99 influenza hemagglutinin bound to Fab 310-63E6
Keywords keywords	hemagglutinin, influenza, antibody, VIRAL PROTEIN, VIRAL PROTEIN-Immune System complex; VIRAL PROTEIN/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	45.36 Å
Radius of gyration Rg (electron density) rg_electron	44.80 Å
Forward intensity I(0) i0	891914000.00
Molecular weight molecular_weight	243380.0 kDa
Excluded volume excluded_volume	302680 Å³
Envelope volume envelope_volume	408900 Å³
Hydration-shell volume shell_volume	74924 Å³
Envelope diameter envelope_diameter	142.2 Å
Shell Rg shell_rg	50.24 Å
Envelope Rg envelope_rg	44.17 Å
Shape Rg shape_rg	44.80 Å
Total Rg total_rg	45.02 Å
Total atoms total_atoms	17145
Residues n_residues	2145
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	146.3 Å
Rg (real space) rg_real	45.19 Å
Rg uncertainty (real space) rg_real_error	0.95 Å
I(0) (real space) i0_real	8.9190e+08
I(0) uncertainty (real space) i0_real_error	1.5280e+07
Rg (reciprocal space) rg_reciprocal	45.36 Å
I(0) (reciprocal space) i0_reciprocal	892100000.0000
Solution quality estimate total_estimate	0.6136
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	54.4 Å
Skewness Skewness skewness	0.158
Kurtosis Kurtosis kurtosis	-0.581
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	91450000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin HA1 chain
Molecular weight formula_weight	35932.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,G
Atom count atom_count	17145

DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCLLKGIAPLQLGNCSVAGWILGNPECELLISKESWSYIVETPNPENGTCYPGYFADYEELREQLSSVSSFERFEIFPKESSWPNHTVTGVSASCSHNGKSSFYRNLLWLTGKNGLYPNLSKSYVNNKEKEVLVLWGVHHPPNIGNQRALYHTENAYVSVVSSHYSRRFTPEIAKRPKVRDQEGRINYYWTLLEPGDTIIFEANGNLIAPWYAFALSRGFGSGIITSNAPMDECDAKCQTPQGAINSSLPFQNVHPVTIGECPKYVRSAKLRMVTGLRNIPS

来源 Source

来源生物 organism	Influenza A virus (strain A/New Zealand:South Canterbury/35/2000 H1N1)
NCBI Class编号 ncbi_taxonomy_id	363066
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Hemagglutinin HA2 chain
Molecular weight formula_weight	26637.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,I

RETRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMNTQFTAVGKEFNKLERRMENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVKNLYEKVKSQLKNNAKEIGNGCFEFYHKCNNECMESVKNGTYDYPKYSEESKLNREKIDGVKYIPEAPRDGQAYVRKDGEWVLLSTFLGSGLNDIFEAQKIEWHEGHHHHHH

来源 Source

来源生物 organism	Influenza A virus (strain A/New Zealand:South Canterbury/35/2000 H1N1)
NCBI Class编号 ncbi_taxonomy_id	363066
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	310-63E6 Fab, Heavy Chain
Molecular weight formula_weight	13394.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,E,J

QVQLVQSGAEVKKPGSSVKVSCTASGGTFSTYQFSWVRQAPGQGLEWMGRIVPIQGMDYAQKFRGRVTITADKWTSTVYMEVTSLRSEDTAVYYCATSRSMYFYYQLDVWGRGTTVTVSS

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	310-63E6 Fab, Light Chain
Molecular weight formula_weight	11810.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

EIVLTQSPGTLSLSPGERATVSCRASQSVTSTFLAWYQQRPGQAPRLLIYGASSRATGIPDRFSGSGSEADFTLTINRLEPEDFAVYYCQQYATSPWTFGQGTKVEIK

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 5 Entity 5 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	15

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7. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	7scnB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	7scnD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	7scnE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7scnF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7scnH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7scnI01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	7scnJ01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7scnK01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7scnL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Resolution resolution	3.02 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	123683

fit	/app/data/saxs_computation/sc/7scn/7scn.fit
pddf	/app/data/pr_computation/sc/7scn/7scn.pr.out
profile	/app/data/saxs_computation/sc/7scn/7scn.dat

Structure of H1 NC99 influenza hemagglutinin bound to Fab 310-63E6

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

Hemagglutinin HA1 chain

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 (5)

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 non-polymer

7. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)