SAXSdb — 7vu5

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

T-cell-specific surface glycoprotein CD28

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 148–188 Chain B； UniProt 148–188	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；310 K；Ionic strength (raw mmCIF value) 25；Pressure 1 NMR sample composition：0.6 mM U-13C; U-15N; 75%-2H CD28_TM, 25 mM MES, 30 mM DMPC, 60 mM DHPC, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.6 mM [U-13C; U-15N] CD28_TM, 25 mM MES, 30 mM acyl chain U-2H DMPC, 60 mM acyl chain U-2H DHPC, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.6 mM U-15N; U-2H CD28_TM, 0.6 mM [U-13C] CD28_TM, 25 mM MES, 30 mM acyl chain U-2H DMPC, 60 mM acyl chain U-2H DHPC, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.2 mM U-15N; 15%-13C CD28_TM, 25 mM MES, 30 mM acyl chain U-2H DMPC, 60 mM acyl chain U-2H DHPC, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 7VU5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1YJD Crystal structure of human CD28 in complex with the Fab fragment of a mitogenic antibody (5.11A1) Deposited 2005-01-14	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 × 6 PDB declaration: hexameric	Chain C 17–152（136 aa） Fragment：Extracellular region	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；294 K；PEG 3350, magnesium formate, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.70 Å R-free 0.282
3WA4 Grb2 SH2 domain/CD28-derived peptide complex Deposited 2013-04-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 189–196（8 aa） Fragment：fragment peptide, UNP residues 190-195	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M HEPES, 1.25M sodium acetate, 0.1M cadmium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.35 Å R-free 0.209
3WA4 Grb2 SH2 domain/CD28-derived peptide complex Deposited 2013-04-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 189–196（8 aa） Fragment：fragment peptide, UNP residues 190-195	Non-standard monomer：Yes (specific site not provided by mmCIF)	CD CADMIUM ION × 1 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M HEPES, 1.25M sodium acetate, 0.1M cadmium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.35 Å R-free 0.209
5AUL PI3K p85 C-terminal SH2 domain/CD28-derived peptide complex Deposited 2015-04-28	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 B 189–196（8 aa） Fragment：UNP residues 189-196	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM Sodium Acetate trihydrate, 200 mM Ammonium Acetate, 30% PEG4000	Resolution 1.10 Å R-free 0.160
5GJH Gads SH2 domain/CD28-derived peptide complex Deposited 2016-06-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 189–196（8 aa） Fragment：UNP residues 189-196	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM HEPES-NaOH, 10% PEG 6000, 20% MPD	Resolution 1.20 Å R-free 0.170
5GJH Gads SH2 domain/CD28-derived peptide complex Deposited 2016-06-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 189–196（8 aa） Fragment：UNP residues 189-196	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM HEPES-NaOH, 10% PEG 6000, 20% MPD	Resolution 1.20 Å R-free 0.170
5GJI PI3K p85 N-terminal SH2 domain/CD28-derived peptide complex Deposited 2016-06-30	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 B 189–196（8 aa） Fragment：UNP residues 189-196	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100mM Sodium acetate trihydrate, 30% PEG MME 2000, 200mM Ammonium sulfate	Resolution 0.90 Å R-free 0.145
6O8D Anti-CD28xCD3 CODV Fab bound to CD28 Deposited 2019-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 33–150（118 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；26% PEG3350, 0.75% myo-inositol, 0.263M potassium citrate tribasic monohydrate	Resolution 3.55 Å R-free 0.356
7PPN SHP2 catalytic domain in complex with CD28 (183-198) phosphopeptide (pTyr-191, p-Thr-195) Deposited 2021-09-14	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 B 183–198（16 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；10% PEG 20000, 100 mM Citrate buffer pH 5.5, 50 mM EDTA	Resolution 1.90 Å R-free 0.207
8S6Z CD28 in complex with the antibody Fab fragment AI3 Deposited 2024-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 19–152（134 aa）	Not recorded	IMD IMIDAZOLE × 4 GOL GLYCEROL × 3 ZN ZINC ION × 13 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；Crystallization trials were set up using the CD28-AI3 Fab at 15.8 mg/mL in phosphate buffered saline (PBS) pH 7.4. Drops were set up using 100 nl protein and 100 nL reservoir solution containing 200 mM zinc acetate, 0.1 M imidazole pH 8.0, 20% w/v PEG 3000.	Resolution 3.05 Å R-free 0.258
8S6Z CD28 in complex with the antibody Fab fragment AI3 Deposited 2024-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 19–152（134 aa）	Not recorded	IMD IMIDAZOLE × 3 GOL GLYCEROL × 3 ZN ZINC ION × 13 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；Crystallization trials were set up using the CD28-AI3 Fab at 15.8 mg/mL in phosphate buffered saline (PBS) pH 7.4. Drops were set up using 100 nl protein and 100 nL reservoir solution containing 200 mM zinc acetate, 0.1 M imidazole pH 8.0, 20% w/v PEG 3000.	Resolution 3.05 Å R-free 0.258
8W2V Solution Structure of the CD28 hinge used in chimeric antigen receptor (CAR) T-cells Deposited 2024-02-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 114–152（39 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 70；Pressure 1 NMR measurement conditions pH 6.5；284 K；Ionic strength (raw mmCIF value) 70；Pressure 1 NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] CD28 hinge, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 20 uM zinc sulphate, 1 mM pefabloc, 0.1 % sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] CD28 hinge, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 20 uM zinc sulphate, 1 mM pefabloc, 0.1 % sodium azide, 100% D2O \| 100% D2O NMR sample composition 0.45 mM [U-100% 13C; U-100% 15N] CD28 hinge, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 20 uM zinc sulphate, 1 mM pefabloc, 0.1 % sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.4 mM [U-100% 15N] CD28 hinge, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 20 uM zinc sulphate, 1 mM pefabloc, 0.1 % sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.28 mM [U-100% 15N] CD28 hinge, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 20 uM zinc sulphate, 1 mM pefabloc, 0.1 % sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

9 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CD28_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–41； UniProt 148–188 Author chain B； PDBConstruct 1–41； UniProt 148–188

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	7vu5
Deposition date deposition_date	2021-11-01
Structure title title	Structure of the transmembrane domain of the CD28 dimer
Keywords keywords	CD28, transmembrane domain, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	19.49 Å
Radius of gyration Rg (electron density) rg_electron	19.49 Å
Forward intensity I(0) i0	182580000.00
Molecular weight molecular_weight	139940.0 kDa
Excluded volume excluded_volume	185990 Å³
Envelope volume envelope_volume	30752 Å³
Hydration-shell volume shell_volume	12904 Å³
Envelope diameter envelope_diameter	78.4 Å
Shell Rg shell_rg	27.04 Å
Envelope Rg envelope_rg	23.39 Å
Shape Rg shape_rg	19.46 Å
Total Rg total_rg	19.89 Å
Total atoms total_atoms	20760
Residues n_residues	1230
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	74.2 Å
Rg (real space) rg_real	20.02 Å
Rg uncertainty (real space) rg_real_error	0.95 Å
I(0) (real space) i0_real	1.8260e+08
I(0) uncertainty (real space) i0_real_error	3.0610e+06
Rg (reciprocal space) rg_reciprocal	19.94 Å
I(0) (reciprocal space) i0_reciprocal	182600000.0000
Solution quality estimate total_estimate	0.6464
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.7 Å
Skewness Skewness skewness	0.637
Kurtosis Kurtosis kurtosis	-0.260
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	50520.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.122; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.058; Smooth: 0.975

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Description description	T-cell-specific surface glycoprotein CD28
Molecular weight formula_weight	4665.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	20760

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

fit	/app/data/saxs_computation/vu/7vu5/7vu5.fit
pddf	/app/data/pr_computation/vu/7vu5/7vu5.pr.out
profile	/app/data/saxs_computation/vu/7vu5/7vu5.dat

Structure of the transmembrane domain of the CD28 dimer

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

T-cell-specific surface glycoprotein CD28

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)