SAXSdb — 7uvf

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

T-cell surface glycoprotein CD8 alpha chain

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 22–141 Chain B； UniProt 22–141	Not recorded	Immunoglobulin heavy chain × 2 Immunoglobulin light chain × 2 GOL GLYCEROL × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；292 K；0.1M ammonium acetate 0.1M Bis-Tris pH6.0 17% PEG 10K	Resolution 2.60 Å R-free 0.259

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7UVF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AKJ COMPLEX OF THE HUMAN MHC CLASS I GLYCOPROTEIN HLA-A2 AND THE T CELL CORECEPTOR CD8 Deposited 1997-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 22–141（120 aa） Fragment：EXTRACELLULAR IGSF DOMAIN, RESIDUES 1 - 120, ALPHA CHAIN Chain E 22–141（120 aa） Fragment：EXTRACELLULAR IGSF DOMAIN, RESIDUES 1 - 120, ALPHA CHAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 12% PEG 20000, 100 MM MES, PH 6.5	Resolution 2.65 Å R-free 0.276
1CD8 CRYSTAL STRUCTURE OF A SOLUBLE FORM OF THE HUMAN T CELL CO-RECEPTOR CD8 AT 2.6 ANGSTROMS RESOLUTION Deposited 1992-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 22–135（114 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1Q69 Solution structure of T-cell surface glycoprotein CD8 alpha chain and Proto-oncogene tyrosine-protein kinase LCK fragments Deposited 2003-08-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 209–227（19 aa） Fragment：Human CD8 alpha	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 5.1；298 K；Pressure ambient NMR sample composition 0.5 mM CD8a-Lck-Zn2+, U-15N,13C; 20 mM acetate, 20 mM NaCl, 0.15% beta-mercaptoethanol \| 95% H2O/5% D2O NMR sample composition 0.5 mM CD8a-Lck-Zn2+, U-15N; 20 mM acetate, 20 mM NaCl, 0.15% beta-mercaptoethanol \| 95% H2O/5% D2O NMR sample composition 0.5 mM CD8a-Lck-Zn2+; 20 mM acetate, 20 mM NaCl, 0.15% beta-mercaptoethanol \| 100% D2O NMR sample composition 1.0 mM CD8a-Lck-Cd2+; 20 mM acetate, 20 mM NaCl, 0.15% beta-mercaptoethanol \| 100% D2O	Resolution not provided
2HP4 Computational design and crystal structure of an enhanced affinity mutant human CD8-alpha-alpha co-receptor Deposited 2006-07-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 22–135（114 aa） Fragment：HLA Co-receptor, Ig-like V-type Chain B 22–135（114 aa） Fragment：HLA Co-receptor, Ig-like V-type	Mutation：C33A/S53N Mutation：C33A/S53N	SO4 SULFATE ION × 5 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；25.5% PEG 8000, 0.085M Sodium Cacodylate, 0.17M Ammonium Sulphate, 15% Glycerol, 3% Ethylene Glycol, pH 6.50, VAPOR DIFFUSION, temperature 291K	Resolution 2.10 Å R-free 0.233
2HP4 Computational design and crystal structure of an enhanced affinity mutant human CD8-alpha-alpha co-receptor Deposited 2006-07-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 22–135（114 aa） Fragment：HLA Co-receptor, Ig-like V-type Chain B 22–135（114 aa） Fragment：HLA Co-receptor, Ig-like V-type	Mutation：C33A/S53N Mutation：C33A/S53N	SO4 SULFATE ION × 10 GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；25.5% PEG 8000, 0.085M Sodium Cacodylate, 0.17M Ammonium Sulphate, 15% Glycerol, 3% Ethylene Glycol, pH 6.50, VAPOR DIFFUSION, temperature 291K	Resolution 2.10 Å R-free 0.233
3QZW Plasticity of human CD8 binding to peptide-HLA-A*2402 Deposited 2011-03-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain G 22–135（114 aa） Fragment：ectodomain (UNP residues 22-135) Chain H 22–135（114 aa） Fragment：ectodomain (UNP residues 22-135)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；0.1M MES monohydrate, pH 6.5, 12% w/v PEG 20000, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.80 Å R-free 0.260
3QZW Plasticity of human CD8 binding to peptide-HLA-A*2402 Deposited 2011-03-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 22–135（114 aa） Fragment：ectodomain (UNP residues 22-135) Chain J 22–135（114 aa） Fragment：ectodomain (UNP residues 22-135)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；0.1M MES monohydrate, pH 6.5, 12% w/v PEG 20000, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.80 Å R-free 0.260
7UMG Crystal structure of human CD8aa-MR1-Ac-6-FP complex Deposited 2022-04-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 22–141（120 aa） Chain D 22–141（120 aa）	Not recorded	30W N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide × 1 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；Na K Phosphate, PEG 1K and NaCl	Resolution 2.40 Å R-free 0.218
8EW6 Anti-human CD8 VHH complex with CD8 alpha Deposited 2022-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain W 22–141（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；15% PEG 3350 and 0.1M succinic acid pH 7.0	Resolution 1.90 Å R-free 0.245

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CD8A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–120； UniProt 22–141 Author chain B； PDBConstruct 1–120； UniProt 22–141

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	7uvf
Deposition date deposition_date	2022-05-01
Structure title title	Crystal structure of ZED8 Fab complex with CD8 alpha
Keywords keywords	imaging, cd8, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	45.41 Å
Radius of gyration Rg (electron density) rg_electron	45.54 Å
Forward intensity I(0) i0	205247000.00
Molecular weight molecular_weight	115930.0 kDa
Excluded volume excluded_volume	144330 Å³
Envelope volume envelope_volume	212240 Å³
Hydration-shell volume shell_volume	40536 Å³
Envelope diameter envelope_diameter	160.9 Å
Shell Rg shell_rg	46.96 Å
Envelope Rg envelope_rg	45.12 Å
Shape Rg shape_rg	45.51 Å
Total Rg total_rg	45.68 Å
Total atoms total_atoms	8178
Residues n_residues	1066
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	159.6 Å
Rg (real space) rg_real	45.90 Å
Rg uncertainty (real space) rg_real_error	2.18 Å
I(0) (real space) i0_real	2.0520e+08
I(0) uncertainty (real space) i0_real_error	4.2170e+06
Rg (reciprocal space) rg_reciprocal	45.42 Å
I(0) (reciprocal space) i0_reciprocal	205100000.0000
Solution quality estimate total_estimate	0.7775
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.0 Å
Skewness Skewness skewness	0.463
Kurtosis Kurtosis kurtosis	-0.476
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8939000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.658; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.553; Smooth: 0.577

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	T-cell surface glycoprotein CD8 alpha chain
Molecular weight formula_weight	14425.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8370

SQFRVSPLDRTWNLGETVELKCQVLLSNPTSGCSWLFQPRGAAASPTFLLYLSQNKPKAAEGLDTQRFSGKRLGDTFVLTLSDFRRENEGYYFCSALSNSIMYFSHFVPVFLPAKPTTTPGNSHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Immunoglobulin heavy chain
Molecular weight formula_weight	23474.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,X

EVQLVQSGAEVKKPGASVKVSCKASGFNIKDTYIHWVRQAPGQGLEWIGRIDPANDNTLYASKFQGRATITADTSTSTAYLELSSLRSEDTAVYYCGRGYGYYVFDHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Immunoglobulin light chain
Molecular weight formula_weight	23437.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,Y

DVQITQSPSSLSASVGDRVTITCRTSRSISQYLAWYQEKPGKTNKLLIYSGSTLQSGIPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQVNEFPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	172

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	7uvfH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7uvfH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7uvfL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7uvfL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7uvfX01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7uvfX02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7uvfY01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7uvfY02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	268.968 Å
Unit-cell length b length_b	59.441 Å
Unit-cell length c length_c	111.377 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.29 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	34.355 Å
R factor r_factor	0.2008
R_work r_work	0.1978
R_free r_free	0.2587

fit	/app/data/saxs_computation/uv/7uvf/7uvf.fit
pddf	/app/data/pr_computation/uv/7uvf/7uvf.pr.out
profile	/app/data/saxs_computation/uv/7uvf/7uvf.dat

Crystal structure of ZED8 Fab complex with CD8 alpha

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

T-cell surface glycoprotein CD8 alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)