9kvd

Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with triple-nAb 3G5, 4H5 and 4C11

Method: ELECTRON MICROSCOPY

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

Spike protein S1

Severe acute respiratory syndrome coronavirus 2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	The heavy chain of 4C11 × 1 The light chain of 4C11 × 1 The heavy chain of 4H5 × 1 The light chain of 4H5 × 1 The heavy chain of 3G5 × 1 The light chain of 3G5 × 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	5
Chains and sequence ranges	Author chain C； PDBConstruct 1–194； UniProt 334–527

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	9kvd
Deposition date deposition_date	2024-12-05
Structure title title	Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with triple-nAb 3G5, 4H5 and 4C11
Keywords keywords	SARS-CoV-2, Neutralizing antibody, Cryo-EM, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
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.

9kvd__assembly_1__model_1

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

Download this curve (.dat)

9kvd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9kvd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.87 Å
Rg (electron density)	31.20 Å
Total Rg	31.84 Å
Atom count	6067
Residues	866
Excluded volume	106020 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9kvd__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 (8)

Entity 1 Entity 1 polymer

Description description	The heavy chain of 4C11
Molecular weight formula_weight	13431.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6067

EVQLVESGGDLVKPGGSLRLSCVASGFTFSRHEMHWVRQAPGEGLEWLSVISETGGTTYYADSVKGRFTISRDNAKNSVFLQMNSLRAEDTAVYFCVRDGGDPAGTVRFFDYWGQGVLVTVSS

Source Source

Source organism organism	Macaca mulatta
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	The light chain of 4C11
Molecular weight formula_weight	11568.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DIQMSQSPSSLSASVGDRVTITCRASQGITSFLNWYQKKPGKAPTLLIYSSNRLASAVPSRFSGSGSGTEFTLTISSLQPEDFATYYCQQYISFPLTFGGGTKVELK

Source Source

Source organism organism	Macaca mulatta
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	The heavy chain of 4H5
Molecular weight formula_weight	13104.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

QVQLQESGPGLVKPSETLSLTCAVSGGSISSGYGWNWIRQPPGKGLEWVGYIYGSSGSTNYNPSLKNRVTISKDASKNQFSLKVRSVTATDTAIYYCARDTYPSAWSWGYWGQGVLVTVSS

Source Source

Source organism organism	Macaca mulatta
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Cricetulus griseus

Entity 4 Entity 4 polymer

Description description	The light chain of 4H5
Molecular weight formula_weight	11750.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

QSVLTQPPSVSGAPGQKVTISCTGSSSNIEVYDVHWYQQLPGTAPKLLIYDNNQRPSGISDRFSGSKSGTSASLAITGLQTEDEADYYCQSYDTSLNAYIFGAGTRLTVL

Source Source

Source organism organism	Macaca mulatta
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Cricetulus griseus

Entity 5 Entity 5 polymer

Description description	Spike protein S1
Molecular weight formula_weight	21772.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	The heavy chain of 3G5
Molecular weight formula_weight	12786.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

QVQLQESGPGLVKPSETLSLTCAVSGVSISSFLWNWIRQPPGKGLEWIGEINGNSGSTYYNPSLKSRVTISKDASKSQFSLILGSVTAADTAVYYCATRDSGPRGVDDYWGQGVLVTVSS

Source Source

Source organism organism	Macaca mulatta
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Cricetulus griseus

Entity 7 Entity 7 polymer

Description description	The light chain of 3G5
Molecular weight formula_weight	12257.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

DIVMTQIPLSLPVTPGEPASISCRSSQTLLHSGSAHTSLDWYLQKPGQSPQLLIYMVSNRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQSVDFPYSFGQGTKVEIK

Source Source

Source organism organism	Macaca mulatta
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Cricetulus griseus

Entity 8 Entity 8 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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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	3.44 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	63542

Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with triple-nAb 3G5, 4H5 and 4C11

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

Spike protein S1

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

9kvd__assembly_1__model_1

9kvd__assembly_1__model_1 | I(q)

9kvd__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

7. Citations (1)

Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with triple-nAb 3G5, 4H5 and 4C11

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

Spike protein S1

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

9kvd__assembly_1__model_1

9kvd__assembly_1__model_1 | I(q)

9kvd__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

7. Citations (1)