SAXSdb — 9ml9

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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 3	M8b-C9 heavy chain × 1 M8b-C9 light chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 water × 3	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–206； UniProt 328–533

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	9ml9
Deposition date deposition_date	2024-12-18
Last revision last_revision	2025-06-04
Structure title title	Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-C9 Fab
Keywords keywords	immune system, neutralizing antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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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.

9ml9__assembly_1__model_1

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

Download this curve (.dat)

9ml9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ml9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.83 Å
Rg (electron density)	30.26 Å
Total Rg	30.94 Å
Atom count	4944
Residues	642
Excluded volume	87805 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ml9__assembly_1__model_1`	trimeric （3）	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 (6)

Entity 1 Entity 1 polymer

Description description	Spike protein S1
Molecular weight formula_weight	24004.9 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	4967

RFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLHHHHHH

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
Common name common_name	SARS-CoV-2, 2019-nCoV, COVID-19 virus
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	M8b-C9 heavy chain
Molecular weight formula_weight	25015.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QSLEESGGDLVKPGTSLTLTCTASGFSFSHNYVMCWVRQAPGKGLECVACIYFGFGDTYYASWAKGRITISKTSSTTVTLQMTSLTAADTATYFCARALGYYIYGDAGDIYIADYFKLWGPGTLVTVSSGQPKAPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

Source Source

Source organism organism	Oryctolagus cuniculus
Common name common_name	rabbit
NCBI taxonomy ID ncbi_taxonomy_id	9986
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	M8b-C9 light chain
Molecular weight formula_weight	23560.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

ADIVMTQTPASVEAAVGGTVTIKCQASQSISKYLAWYQQKPGQPPKLLIFEASTLESGVPSRFKGRGSGTEFTLTISDLECADAATYYCQGYYYSSHSYVFGGGTEVVVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Oryctolagus cuniculus
Common name common_name	rabbit
NCBI taxonomy ID ncbi_taxonomy_id	9986
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 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

Entity 5 Entity 5 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	23

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Unit-cell length a length_a	108.159 Å
Unit-cell length b length_b	127.194 Å
Unit-cell length c length_c	75.431 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	127.72 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	2.590 Å
Low-resolution limit resolution_low	37.990 Å
R factor r_factor	0.2286
R_work r_work	0.2259
R_free r_free	0.2572

Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-C9 Fab

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

9ml9__assembly_1__model_1

9ml9__assembly_1__model_1 | I(q)

9ml9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-C9 Fab

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

9ml9__assembly_1__model_1

9ml9__assembly_1__model_1 | I(q)

9ml9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)