8s6z

CD28 in complex with the antibody Fab fragment AI3

Method: X-RAY DIFFRACTION D_max: 141.2 Å Quality: GOOD

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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	Other combination Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 19–152	Not recorded	Heavy chain Fab fragment of AI3 antibody × 1 Light chain of AI3 antibody × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 19–152	Not recorded	Heavy chain Fab fragment of AI3 antibody × 1 Light chain of AI3 antibody × 1 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

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 8S6Z	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 oligomeric state Different ligand/ion 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 ligand/ion 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 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 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 ligand/ion 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 ligand/ion 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 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 oligomeric state Different ligand/ion 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 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
7VU5 Structure of the transmembrane domain of the CD28 dimer Deposited 2021-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 148–188（41 aa） Chain B 148–188（41 aa）	Not recorded	No recorded non-water small molecule	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
8W2V Solution Structure of the CD28 hinge used in chimeric antigen receptor (CAR) T-cells Deposited 2024-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CD28_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–134； UniProt 19–152 Author chain F； PDBConstruct 1–134； UniProt 19–152

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8s6z
Deposition date deposition_date	2024-02-28
Structure title title	CD28 in complex with the antibody Fab fragment AI3
Keywords keywords	Antibody, Complex, CD28, 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	36.29 Å
Radius of gyration Rg (electron density) rg_electron	36.35 Å
Forward intensity I(0) i0	257770000.00
Molecular weight molecular_weight	125820.0 kDa
Excluded volume excluded_volume	155670 Å³
Envelope volume envelope_volume	202340 Å³
Hydration-shell volume shell_volume	48866 Å³
Envelope diameter envelope_diameter	147.7 Å
Shell Rg shell_rg	40.22 Å
Envelope Rg envelope_rg	36.61 Å
Shape Rg shape_rg	36.33 Å
Total Rg total_rg	36.68 Å
Total atoms total_atoms	8758
Residues n_residues	1090
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	141.2 Å
Rg (real space) rg_real	36.50 Å
Rg uncertainty (real space) rg_real_error	1.65 Å
I(0) (real space) i0_real	2.5780e+08
I(0) uncertainty (real space) i0_real_error	4.9200e+06
Rg (reciprocal space) rg_reciprocal	36.37 Å
I(0) (reciprocal space) i0_reciprocal	257700000.0000
Solution quality estimate total_estimate	0.7928
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.7 Å
Skewness Skewness skewness	0.612
Kurtosis Kurtosis kurtosis	0.402
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	32000000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.518; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.820; Smooth: 0.928

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Heavy chain Fab fragment of AI3 antibody
Molecular weight formula_weight	23468.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	8785

EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKSYGAFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

来源 Source

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

Entity 2 Entity 2 polymer

Description description	Light chain of AI3 antibody
Molecular weight formula_weight	24212.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQNLRPPETFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

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

Entity 3 Entity 3 polymer

Description description	T-cell-specific surface glycoprotein CD28
Molecular weight formula_weight	15159.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

NKILVKQSPMLVAYDNAVNLSCKYSYNLFSREFRASLHKGLDSAVEVCVVYGNYSQQLQVYSKTGFNCDGKLGNESVTFYLQNLYVNQTDIYFCKIEVMYPPPYLDNEKSNGTIIHVKGKHLCPSPLFPGPSKP

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	Cricetulus griseus

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	26

Entity 8 Entity 8 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	9

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	27

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8. Citations (1)

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Unit-cell length a length_a	76.874 Å
Unit-cell length b length_b	117.939 Å
Unit-cell length c length_c	145.719 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.050 Å
Low-resolution limit resolution_low	91.843 Å
R factor r_factor	—
R_work r_work	0.1975
R_free r_free	0.2575

fit	/app/data/saxs_computation/s6/8s6z/8s6z.fit
pddf	/app/data/pr_computation/s6/8s6z/8s6z.pr.out
profile	/app/data/saxs_computation/s6/8s6z/8s6z.dat

CD28 in complex with the antibody Fab fragment AI3

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (9)

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 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)