SAXSdb — 8tmy

▼

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

;Stem helix peptide of Spike protein S2' ;

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Neutralizing antibody CHM-16 Heavy Chain × 1 Neutralizing antibody CHM-16 Light Chain × 1 CITRATE ANION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Neutralizing antibody CHM-16 Heavy Chain × 1 Neutralizing antibody CHM-16 Light Chain × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Neutralizing antibody CHM-16 Heavy Chain × 1 Neutralizing antibody CHM-16 Light Chain × 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	1
Chains and sequence ranges	Author chain M； PDBConstruct 1–25； UniProt 1140–1164 Author chain N； PDBConstruct 1–25； UniProt 1140–1164 Author chain S； PDBConstruct 1–25； UniProt 1140–1164

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8tmy
Deposition date deposition_date	2023-07-31
Structure title title	Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody CHM-16
Keywords keywords	Antibody, SARS-CoV-2, Coronavirus, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

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.

8tmy__assembly_1__model_1

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

Download this curve (.dat)

8tmy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8tmy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.93 Å
Rg (electron density)	24.93 Å
Total Rg	25.80 Å
Atom count	3398
Residues	444
Excluded volume	59987 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8tmy__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8tmy__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`8tmy__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	;Stem helix peptide of Spike protein S2' ;
Molecular weight formula_weight	2981.3 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,S
Atom count atom_count	10123

PLQPELDSFKEELDKYFKNHTSPDV

Entity 2 Entity 2 polymer

Description description	Neutralizing antibody CHM-16 Heavy Chain
Molecular weight formula_weight	23568.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,A,C

EEQLVESGGGLVQPGGSLRLSCTASGFTLSTYFMFWVRQPPGKGLEWVSGINLGGDKTWSTDSVKGRFTTSKENAKNTLYLQMDSLRPEDTAVYYCARLRSQRGFDHWGQGALVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Source Source

Source organism organism	Macaca mulatta
Common name common_name	Rhesus monkey
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Neutralizing antibody CHM-16 Light Chain
Molecular weight formula_weight	23322.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

DIQMTQSPSSLSASVGDRVTFTCRASQGVNNWLAWYQQKPGKAPKLLIYRASNLETGVPSRFSGSGSGTEFTLTISSLQPEDIATYYCQQHDNFPYTFGQGTKVVIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTQGTTSVTKSFNRGEC

Source Source

Source organism organism	Macaca mulatta
Common name common_name	Rhesus monkey
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	1

▶

Unit-cell length a length_a	73.456 Å
Unit-cell length b length_b	73.677 Å
Unit-cell length c length_c	330.624 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	12

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.070 Å
Low-resolution limit resolution_low	33.060 Å
R factor r_factor	0.2460
R_work r_work	0.2432
R_free r_free	0.2863

Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody CHM-16

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

;Stem helix peptide of Spike protein S2' ;

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

8tmy__assembly_1__model_1

8tmy__assembly_1__model_1 | I(q)

8tmy__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

7. Citations (1)

Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody CHM-16

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

;Stem helix peptide of Spike protein S2' ;

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

8tmy__assembly_1__model_1

8tmy__assembly_1__model_1 | I(q)

8tmy__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

7. Citations (1)