SAXSdb — 9jeb

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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 2	N1 scFv × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	N1 scFv × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–197； UniProt 333–529 Author chain D； PDBConstruct 1–197； UniProt 333–529

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	9jeb
Deposition date deposition_date	2024-09-03
Structure title title	Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv N1
Keywords keywords	SARS-CoV-2, RBD, antibody, scFv, VIRAL PROTEIN, 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.

9jeb__assembly_1__model_1

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

Download this curve (.dat)

9jeb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9jeb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.89 Å
Rg (electron density)	24.06 Å
Total Rg	24.93 Å
Atom count	3342
Residues	428
Excluded volume	59057 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9jeb__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9jeb__assembly_2__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	N1 scFv
Molecular weight formula_weight	26344.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	7532

EVHLVESGGGVVQPGRSLKLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVISHDGSSKFYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKEFYDSGNYRPELFDYWGQGTTITVSSGGGGSGGGGSGGGGSEIVLTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPPWTFGQGTKVEIK

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia

Entity 2 Entity 2 polymer

Description description	Spike protein S1
Molecular weight formula_weight	22131.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKK

Source Source

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

Entity 3 Entity 3 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 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	819

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Unit-cell length a length_a	190.399 Å
Unit-cell length b length_b	190.399 Å
Unit-cell length c length_c	60.138 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 62
Space-group number int_tables_number	171
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	32.980 Å
R factor r_factor	0.1794
R_work r_work	0.1783
R_free r_free	0.2059

Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv N1

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

9jeb__assembly_1__model_1

9jeb__assembly_1__model_1 | I(q)

9jeb__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv N1

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

9jeb__assembly_1__model_1

9jeb__assembly_1__model_1 | I(q)

9jeb__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)