1yuk

The crystal structure of the PSI/Hybrid domain/ I-EGF1 segment from the human integrin beta2 at 1.8 resolution

Method: X-RAY DIFFRACTION D_max: 87.7 Å Quality: REASONABLE

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

Integrin beta-2 A 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 23–125 Chain B； UniProt 365–482	Fragment：PSI domain Fragment：I-EGF domain	NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；18% PEG 8000, 0.2M calcium acetate, 0.1M Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.253

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 1YUK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1L3Y INTEGRIN EGF-LIKE MODULE 3 FROM THE BETA-2 SUBUNIT Deposited 2002-03-03	Different construct Different mutation/modification 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 535–574（40 aa） Fragment：RESIDUES 535-574	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.2；298 K；Ionic strength (raw mmCIF value) 5mM NaPO4；Pressure ambient NMR sample composition 1 mM I-EGF3 U-15N, 5 mM NaPO4 \| 90% H2O/10% D2O NMR sample composition 1 mM I-EGF3, 5 mM NaPO4 \| 100% D2O	Resolution not provided
2JF1 CRYSTAL STRUCTURE OF THE FILAMIN A REPEAT 21 COMPLEXED WITH THE INTEGRIN BETA2 CYTOPLASMIC TAIL PEPTIDE Deposited 2007-01-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain T 735–769（35 aa） Fragment：RESIDUES 735-769	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；1.6-1.58 M AMMONIUM SULPHATE, 0.1 M NA-ACETATE PH 4.6	Resolution 2.20 Å R-free 0.278
2P26 Structure of the PHE2 and PHE3 fragments of the integrin beta2 subunit Deposited 2007-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–122（100 aa） Fragment：PHE2 and PHE3 Chain A 362–535（174 aa） Fragment：PHE2 and PHE3	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；0.2M Magnesium acetate, 0.1M sodium acetate, pH4.6, 18% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.75 Å R-free 0.253
2P28 Structure of the PHE2 and PHE3 fragments of the integrin beta2 subunit Deposited 2007-03-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–122（100 aa） Fragment：PHE2 fragment Chain B 362–574（213 aa） Fragment：PHE3 fragment	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M ammonium sulphate, 15% PEG4000, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.20 Å R-free 0.308
3K6S Structure of integrin alphaXbeta2 ectodomain Deposited 2009-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 23–700（678 aa） Fragment：residues 23-700	Not recorded	MAN alpha-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 4 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；277 K；0.55M tri-sodium citrate, 0.1M imidazole, pH 6.5, EVAPORATION, temperature 277K	Resolution 3.50 Å R-free 0.335
3K6S Structure of integrin alphaXbeta2 ectodomain Deposited 2009-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 23–700（678 aa） Fragment：residues 23-700	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；277 K；0.55M tri-sodium citrate, 0.1M imidazole, pH 6.5, EVAPORATION, temperature 277K	Resolution 3.50 Å R-free 0.335
3K6S Structure of integrin alphaXbeta2 ectodomain Deposited 2009-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 23–700（678 aa） Fragment：residues 23-700	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；277 K；0.55M tri-sodium citrate, 0.1M imidazole, pH 6.5, EVAPORATION, temperature 277K	Resolution 3.50 Å R-free 0.335
3K6S Structure of integrin alphaXbeta2 ectodomain Deposited 2009-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 23–700（678 aa） Fragment：residues 23-700	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；277 K；0.55M tri-sodium citrate, 0.1M imidazole, pH 6.5, EVAPORATION, temperature 277K	Resolution 3.50 Å R-free 0.335
3K6S Structure of integrin alphaXbeta2 ectodomain Deposited 2009-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain B 23–700（678 aa） Fragment：residues 23-700 Chain D 23–700（678 aa） Fragment：residues 23-700 Chain F 23–700（678 aa） Fragment：residues 23-700 Chain H 23–700（678 aa） Fragment：residues 23-700	Not recorded	MAN alpha-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 CA CALCIUM ION × 16 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；277 K；0.55M tri-sodium citrate, 0.1M imidazole, pH 6.5, EVAPORATION, temperature 277K	Resolution 3.50 Å R-free 0.335
3K71 Structure of integrin alphaX beta2 ectodomain Deposited 2009-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 23–700（678 aa） Fragment：residues 23-700	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.55M tri-sodium citrate, 0.05M MgCl2, 0.1M imidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.95 Å R-free 0.373
3K71 Structure of integrin alphaX beta2 ectodomain Deposited 2009-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 23–700（678 aa） Fragment：residues 23-700	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.55M tri-sodium citrate, 0.05M MgCl2, 0.1M imidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.95 Å R-free 0.373
3K71 Structure of integrin alphaX beta2 ectodomain Deposited 2009-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 23–700（678 aa） Fragment：residues 23-700	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.55M tri-sodium citrate, 0.05M MgCl2, 0.1M imidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.95 Å R-free 0.373
3K71 Structure of integrin alphaX beta2 ectodomain Deposited 2009-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 23–700（678 aa） Fragment：residues 23-700	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 4 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.55M tri-sodium citrate, 0.05M MgCl2, 0.1M imidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.95 Å R-free 0.373
3K71 Structure of integrin alphaX beta2 ectodomain Deposited 2009-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain B 23–700（678 aa） Fragment：residues 23-700 Chain D 23–700（678 aa） Fragment：residues 23-700 Chain F 23–700（678 aa） Fragment：residues 23-700 Chain H 23–700（678 aa） Fragment：residues 23-700	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 CA CALCIUM ION × 16 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.55M tri-sodium citrate, 0.05M MgCl2, 0.1M imidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.95 Å R-free 0.373
3K72 Structure of integrin alphaX beta2 Deposited 2009-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 23–700（678 aa） Fragment：residues 23-700	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；0.915M sodium/potassium phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.70 Å R-free 0.335
3K72 Structure of integrin alphaX beta2 Deposited 2009-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 23–700（678 aa） Fragment：residues 23-700	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 4 MAN alpha-D-mannopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；0.915M sodium/potassium phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.70 Å R-free 0.335
3K72 Structure of integrin alphaX beta2 Deposited 2009-10-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain B 23–700（678 aa） Fragment：residues 23-700 Chain D 23–700（678 aa） Fragment：residues 23-700	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 CA CALCIUM ION × 16 MAN alpha-D-mannopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；0.915M sodium/potassium phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.70 Å R-free 0.335
4NEH An internal ligand-bound, metastable state of a leukocyte integrin, aXb2 Deposited 2013-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 23–696（674 aa） Fragment：CD18	Mutation：N190D, N232K, V674C	CA CALCIUM ION × 5 MG MAGNESIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；297 K；6% PEG 8000, 0.2 M Mg acetate, 0.1 M Na cacodylate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.75 Å R-free 0.225
4NEN An internal ligand-bound, metastable state of a leukocyte integrin, aXb2 Deposited 2013-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 23–696（674 aa） Fragment：CD18	Mutation：N190D, N232K and V696C	CA CALCIUM ION × 5 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；297 K；6% PEG 8000, 0.2 M Mg acetate, 0.1 M Na cacodylate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.90 Å R-free 0.264
5E6R Structures of leukocyte integrin aLb2: The aI domain, the headpiece, and the pocket for the internal ligand Deposited 2015-10-10	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 23–482（460 aa） Fragment：UNP residues 23-482	Mutation：N232R	MG MAGNESIUM ION × 1 CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES pH 6.5, 15% PEG 3350	Resolution 2.90 Å R-free 0.229
5E6S Structures of leukocyte integrin aLB2: The aI domain, the headpiece, and the pocket for the internal ligand Deposited 2015-10-10	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 23–482（460 aa） Fragment：UNP residues 23-482	Not recorded	MG MAGNESIUM ION × 1 CA CALCIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；0.1 M Tris, pH 8, 0.1 M NaCl, and 8% polyethylene glycol (PEG) 20,000	Resolution 2.15 Å R-free 0.234
5E6S Structures of leukocyte integrin aLB2: The aI domain, the headpiece, and the pocket for the internal ligand Deposited 2015-10-10	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 23–482（460 aa） Fragment：UNP residues 23-482	Not recorded	MG MAGNESIUM ION × 1 CA CALCIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；0.1 M Tris, pH 8, 0.1 M NaCl, and 8% polyethylene glycol (PEG) 20,000	Resolution 2.15 Å R-free 0.234
5E6S Structures of leukocyte integrin aLB2: The aI domain, the headpiece, and the pocket for the internal ligand Deposited 2015-10-10	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 F 23–482（460 aa） Fragment：UNP residues 23-482	Not recorded	MG MAGNESIUM ION × 1 CA CALCIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；0.1 M Tris, pH 8, 0.1 M NaCl, and 8% polyethylene glycol (PEG) 20,000	Resolution 2.15 Å R-free 0.234
5E6S Structures of leukocyte integrin aLB2: The aI domain, the headpiece, and the pocket for the internal ligand Deposited 2015-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 23–482（460 aa） Fragment：UNP residues 23-482 Chain D 23–482（460 aa） Fragment：UNP residues 23-482 Chain F 23–482（460 aa） Fragment：UNP residues 23-482	Not recorded	MG MAGNESIUM ION × 3 CA CALCIUM ION × 15 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；0.1 M Tris, pH 8, 0.1 M NaCl, and 8% polyethylene glycol (PEG) 20,000	Resolution 2.15 Å R-free 0.234
5E6U Structures of leukocyte integrin aLb2: The aI domain, the headpiece, and the pocket for the internal ligand Deposited 2015-10-10	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 23–482（460 aa） Fragment：UNP residues 23-482	Not recorded	MG MAGNESIUM ION × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M Mg-formate dehydrate and 15% PEG 3350	Resolution 2.50 Å R-free 0.226
5E6V Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin b2 Subunit Deposited 2015-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–125（103 aa） Fragment：UNP residues 23-125, 365-482 Chain A 365–482（118 aa） Fragment：UNP residues 23-125, 365-482	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å R-free 0.229
5E6W Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin b2 Subunit Deposited 2015-10-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–122（100 aa） Fragment：UNP residues 23-122, 362-574 Chain A 362–574（213 aa） Fragment：UNP residues 23-122, 362-574	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.270
5E6X Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin b2 Subunit Deposited 2015-10-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–122（100 aa） Fragment：UNP residues 23-122 and 362 535 Chain A 362–535（174 aa） Fragment：UNP residues 23-122 and 362 535	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.75 Å R-free 0.245
5ES4 RE-REFINEMENT OF INTEGRIN ALPHAXBETA2 ECTODOMAIN IN THE CLOSED/BENT CONFORMATION Deposited 2015-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 23–696（674 aa） Fragment：UNP residues 23-696	Not recorded	CA CALCIUM ION × 4 MG MAGNESIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.55M TRI-SODIUM CITRATE, 0.1M IMIDAZOLE, PH 6.5, EVAPORATION, TEMPERATURE 277K	Resolution 3.30 Å R-free 0.307
5ES4 RE-REFINEMENT OF INTEGRIN ALPHAXBETA2 ECTODOMAIN IN THE CLOSED/BENT CONFORMATION Deposited 2015-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 23–696（674 aa） Fragment：UNP residues 23-696	Not recorded	CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.55M TRI-SODIUM CITRATE, 0.1M IMIDAZOLE, PH 6.5, EVAPORATION, TEMPERATURE 277K	Resolution 3.30 Å R-free 0.307
5ES4 RE-REFINEMENT OF INTEGRIN ALPHAXBETA2 ECTODOMAIN IN THE CLOSED/BENT CONFORMATION Deposited 2015-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 23–696（674 aa） Fragment：UNP residues 23-696	Not recorded	CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.55M TRI-SODIUM CITRATE, 0.1M IMIDAZOLE, PH 6.5, EVAPORATION, TEMPERATURE 277K	Resolution 3.30 Å R-free 0.307
5ES4 RE-REFINEMENT OF INTEGRIN ALPHAXBETA2 ECTODOMAIN IN THE CLOSED/BENT CONFORMATION Deposited 2015-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 23–696（674 aa） Fragment：UNP residues 23-696	Not recorded	CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.55M TRI-SODIUM CITRATE, 0.1M IMIDAZOLE, PH 6.5, EVAPORATION, TEMPERATURE 277K	Resolution 3.30 Å R-free 0.307
5XR1 Structure of FLN IG21 domain in complex with C-terminal peptide of beta-2 Deposited 2017-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 752–763（12 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.2；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1 NMR sample composition 300 uM [U-13C; U-15N] FLN IG21 domain, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5ZAZ Solution structure of integrin b2 monomer tranmembrane domain in bicelle Deposited 2018-02-09	Different construct Different mutation/modification 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 689–739（51 aa）	Mutation：C695S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；303 K；Ionic strength (raw mmCIF value) 20；Pressure 1 NMR sample composition 0.6 mM [U-13C; U-15N] integrin b2, 20 mM Bis-Tris, 240 mM DHPC, 48 mM POPC, 24 mM POPG, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9ECL Structure of the human integrin beta2 transmembrane domain Deposited 2024-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 696–735（40 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；313.2 K；Ionic strength (raw mmCIF value) 0.025；Pressure 1 NMR sample composition 1.2 mM [U-100% 13C; U-100% 15N; U-80% 2H] alphaX peptide, 350 mM 1,2-dihexanoyl-sn-glycero-3-phosphoholine, 105 mM 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 25 mM HEPES, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
9RM9 Cryo-EM structure of alphaM/beta2 headpiece complex without alphaM I-domain - the consensus map from alphaM/beta2:C3d-anti-CR3-Nb headpiece complex Deposited 2025-06-18	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 × 2 PDB declaration: dimeric	Chain B 23–482（460 aa）	Not recorded	CA CALCIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MN MANGANESE (II) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；0.02 % w/v CHAPS added to sample just before vitrification	Resolution 2.60 Å
9T3Y Cryo-EM structure of alphaM/beta2:C3d-anti-CR3-Nb headpiece complex (HPO2 3D class reconstruction) Deposited 2025-10-30	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 B 23–482（460 aa）	Not recorded	CA CALCIUM ION × 5 MN MANGANESE (II) ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；0.02 % w/v CHAPS added to sample just before vitrification	Resolution 3.44 Å
9T5V Cryo-EM structure of alphaM/beta2:C3d-anti-CR3-Nb headpiece complex (HPO1 3D class reconstruction) Deposited 2025-11-06	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 B 23–485（463 aa）	Not recorded	CA CALCIUM ION × 5 MN MANGANESE (II) ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；0.02 % w/v CHAPS added to sample just before vitrification	Resolution 3.06 Å
9T5W Cryo-EM structure of mutant R61H alphaM/beta2 headpiece complex Deposited 2025-11-06	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 × 2 PDB declaration: dimeric	Chain B 23–482（460 aa）	Not recorded	CA CALCIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MN MANGANESE (II) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；0.02 % w/v CHAPS added to sample just before vitrification	Resolution 2.74 Å
9T5Z Cryo-EM structure of alphaM/beta2:MEM148-Fab headpiece complex (without alphaM I-domain) Deposited 2025-11-06	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 × 4 PDB declaration: tetrameric	Chain B 23–485（463 aa）	Not recorded	CA CALCIUM ION × 5 MN MANGANESE (II) ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

24 other PDB entries and 40 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ITB2_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–103； UniProt 23–125 Author chain B； PDBConstruct 1–118； UniProt 365–482

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	1yuk
Deposition date deposition_date	2005-02-14
Structure title title	The crystal structure of the PSI/Hybrid domain/ I-EGF1 segment from the human integrin beta2 at 1.8 resolution
Keywords keywords	Integrin beta2, hybrid domain, PSI domain, I-EGF domain, crystal structure of PSI/HYBRID/I-EGF1, CELL ADHESION; CELL ADHESION
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	23.44 Å
Radius of gyration Rg (electron density) rg_electron	23.08 Å
Forward intensity I(0) i0	12053800.00
Molecular weight molecular_weight	24246.0 kDa
Excluded volume excluded_volume	29593 Å³
Envelope volume envelope_volume	38082 Å³
Hydration-shell volume shell_volume	15325 Å³
Envelope diameter envelope_diameter	84.8 Å
Shell Rg shell_rg	27.76 Å
Envelope Rg envelope_rg	23.43 Å
Shape Rg shape_rg	23.12 Å
Total Rg total_rg	23.59 Å
Total atoms total_atoms	1687
Residues n_residues	214
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	87.7 Å
Rg (real space) rg_real	23.77 Å
Rg uncertainty (real space) rg_real_error	1.14 Å
I(0) (real space) i0_real	1.2050e+07
I(0) uncertainty (real space) i0_real_error	1.9530e+05
Rg (reciprocal space) rg_reciprocal	23.69 Å
I(0) (reciprocal space) i0_reciprocal	12050000.0000
Solution quality estimate total_estimate	0.7449
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.9 Å
Skewness Skewness skewness	0.572
Kurtosis Kurtosis kurtosis	-0.349
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2891000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.477; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.250; Smooth: 1.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Integrin beta-2 A chain
Molecular weight formula_weight	11386.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1906

QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPTSLAETQEDHNGGQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGY

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	Integrin beta-2 B chain
Molecular weight formula_weight	13483.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SRVFLDHNALPDTLKVTYDSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVLPQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCEHH

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 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-alpha-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	219

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	1yukA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1680 — ligand-binding face of the semaphorins, domain 2
Homologous superfamily homologous superfamily	10 — ligand-binding face of the semaphorins, domain 2

Domain ID domain_id	1yukA02
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	50 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1yukB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1510 — ntegrin, alpha v. Chain A, domain 3

Domain ID domain_id	1yukB02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

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8. Citations (1)

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Unit-cell length a length_a	58.600 Å
Unit-cell length b length_b	31.818 Å
Unit-cell length c length_c	74.950 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2340
R_work r_work	0.2340
R_free r_free	0.2530

fit	/app/data/saxs_computation/yu/1yuk/1yuk.fit
pddf	/app/data/pr_computation/yu/1yuk/1yuk.pr.out
profile	/app/data/saxs_computation/yu/1yuk/1yuk.dat

The crystal structure of the PSI/Hybrid domain/ I-EGF1 segment from the human integrin beta2 at 1.8 resolution

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

Integrin beta-2 A 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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)