7wp8

Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK1628x in complex with three neutralizing antibodies

Method: ELECTRON MICROSCOPY

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

Spike glycoprotein

Severe acute respiratory syndrome coronavirus 2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 其他Polymer 1	83H7 light chain × 1 83H7 heavy chain × 1 2B4 heavy chain × 1 2B4 light chain × 1 85F7 heavy chain × 1 85F7 light chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPIKE_SARS2
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–183； UniProt 336–518

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	7wp8
Deposition date deposition_date	2022-01-23
Structure title title	Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK1628x in complex with three neutralizing antibodies
Keywords keywords	SARS-CoV-2, spike, vaccine, neutralizing antibody, Cryo-EM, VIRAL PROTEIN, IMMUNE SYSTEM-VIRAL PROTEIN complex; IMMUNE SYSTEM/VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7wp8__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7wp8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7wp8__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.03 Å
Rg (electron density)	31.42 Å
Total Rg	32.28 Å
Atom count	6797
Residues	861
Excluded volume	120070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7wp8__assembly_1__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	83H7 light chain
Molecular weight formula_weight	11428.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	6797

VMTQSHKFLSTSVGDRVNITCKASQDVDTAVAWYQQKPGQSPKLLISWASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLADYFCQQYSPYPYTFGGGTKLEI

Entity 2 Entity 2 polymer

Description description	83H7 heavy chain
Molecular weight formula_weight	13027.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

QLAQSGAELARPGASVKLSCKASGYTFTRYWMQWVKQRPGQGLEWIGAIYPGDGDSRYTQKFKGKATLTADKSSSTAYMQLSSLASEDSAVYYCARRNYYGYDAFAYWGQGTLVTVSA

Entity 3 Entity 3 polymer

Description description	2B4 heavy chain
Molecular weight formula_weight	13681.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

QVQLQQPGAELVRPGASVKLSCKASGYTFTSYWMNWVKQRPEQGLEWIGRIDPYDSETHYNQKFKDKAILTVDKSSTTAYMQLSSLTSEDSAVYYCARWGTVEWFFDYWGQGTTLTVSQ

Entity 4 Entity 4 polymer

Description description	Spike glycoprotein
Molecular weight formula_weight	20803.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

CPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGTIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELL

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Cricetulus griseus

Entity 5 Entity 5 polymer

Description description	2B4 light chain
Molecular weight formula_weight	12449.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

DIVMTQSPSSLAMSVGQKVTMSCKSSQSLLNSYNQENYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCQQHYSTPFTFGSGTKLEIK

Entity 6 Entity 6 polymer

Description description	85F7 heavy chain
Molecular weight formula_weight	13159.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLQQSGPELVKPGASVRISCKASGYTFTSYYIHWVKQRPGQGLEWIGWIYPGNVKSIYNEKFKGKATLTADKSSNTAYMQLSSLTSEDSAVYFCAGEEHGNYFDFWGQGTTLTVSQ

Entity 7 Entity 7 polymer

Description description	85F7 light chain
Molecular weight formula_weight	11278.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

QIVLSQSPTILSASPGEKVTMTCRANSSVGFMHWCQQKPGSSPKPWIYATSNLASGVPGRFSGSGSGTSYSLTISRVEAEDAATYYCQQWSSDPPTFGSGTKLEIK

Entity 8 Entity 8 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	1

Entity 9 Entity 9 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	1

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	7wp8C01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7wp8D01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7wp8E01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7wp8G01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7wp8H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7wp8L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.88 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	115589

Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK1628x in complex with three neutralizing antibodies

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

Spike glycoprotein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7wp8__assembly_1__model_1

7wp8__assembly_1__model_1 | I(q)

7wp8__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 branched

Entity 9 Entity 9 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK1628x in complex with three neutralizing antibodies

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

Spike glycoprotein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7wp8__assembly_1__model_1

7wp8__assembly_1__model_1 | I(q)

7wp8__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 branched

Entity 9 Entity 9 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)