8ce6

Crystal structure of human Cd11b I domain in P212121 space group

Method: X-RAY DIFFRACTION D_max: 52.6 Å Quality: GOOD

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

Integrin alpha-M

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 149–337	Not recorded	SO4 SULFATE ION × 7 GOL GLYCEROL × 7 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.15M ammonium sulfate 25% PEG4000 15% glycerol	Resolution 1.58 Å R-free 0.208

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 8CE6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BHO MAC-1 I DOMAIN MAGNESIUM COMPLEX Deposited 1998-06-10	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 1 149–337（189 aa） Fragment：MAC-1 ALPHA DOMAIN Chain 2 149–337（189 aa） Fragment：MAC-1 ALPHA DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；CRYSTALS WERE GROWN BY VAPOR DIFFUSION ON SITTING DROP BRIDGES. THE WELL MIX OF 20-24% PEG6000 BUFFERED WITH 100 MM NA ACETATE PH 5.0 WAS MIXED 1:1 WITH 3 UL OF I DOMAIN PROTEIN (20-30 MG/ML, 50 MM HEPES PH 7.0, 0.025% NA AZIDE). CRYSTALS WERE STABLIZED IN 100MM MGCL2, 100 MM NA ACETATE 5.0, 26% PEG6000 FOR DATA COLLECTION., vapor diffusion - sitting drop	Resolution 2.70 Å
1BHQ MAC-1 I DOMAIN CADMIUM COMPLEX Deposited 1998-06-10	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 1 149–337（189 aa） Fragment：MAC-1 ALPHA DOMAIN Chain 2 149–337（189 aa） Fragment：MAC-1 ALPHA DOMAIN	Not recorded	CD CADMIUM ION × 3 ACE ACETYL GROUP × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；CRYSTALS WERE GROWN BY VAPOR DIFFUSION ON SITTING DROP BRIDGES. THE WELL MIX OF 20-24% PEG6000 BUFFERED WITH 100 MM NA ACETATE PH 5.0 WAS MIXED 1:1 WITH 3 UL OF I DOMAIN PROTEIN (20-30 MG/ML, 50 MM HEPES PH 7.0, 0.025% NA AZIDE). CRYSTALS WERE STABLIZED IN 10MM CDCL2, 100 MM NA ACETATE 5.0, 26% PEG6000 FOR DATA COLLECTION., vapor diffusion - sitting drop	Resolution 2.70 Å
1IDN MAC-1 I DOMAIN METAL FREE Deposited 1998-06-10	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 1 149–337（189 aa） Fragment：MAC-1 ALPHA DOMAIN Chain 2 149–337（189 aa） Fragment：MAC-1 ALPHA DOMAIN	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 X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；CRYSTALS WERE GROWN BY VAPOR DIFFUSION ON SITTING DROP BRIDGES. THE WELL MIX OF 20-24% PEG6000 BUFFERED WITH 100 MM NA ACETATE PH 5.0 WAS MIXED 1:1 WITH 3 UL OF I DOMAIN PROTEIN (20-30 MG/ML, 50 MM HEPES PH 7.0, 0.025% NA AZIDE). CRYSTALS WERE STABLIZED IN 100 MM NA ACETATE 5.0; 26% PEG6000 FOR DATA COLLECTION., vapor diffusion - sitting drop	Resolution 2.70 Å
1IDO I-DOMAIN FROM INTEGRIN CR3, MG2+ BOUND Deposited 1996-03-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 148–331（184 aa） Fragment：I-DOMAIN	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 1.70 Å
1JLM I-DOMAIN FROM INTEGRIN CR3, MN2+ BOUND Deposited 1996-04-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 143–334（192 aa） Fragment：I-DOMAIN	Not recorded	MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1M1U AN ISOLEUCINE-BASED ALLOSTERIC SWITCH CONTROLS AFFINITY AND SHAPE SHIFTING IN INTEGRIN CD11B A-DOMAIN Deposited 2002-06-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 139–331（193 aa） Fragment：CD11b A-domain, Residues 123-315	Mutation：C128S	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；298 K；15% PEG8K, 0.1M Tris-HCl 8.2, 5mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.248
1MF7 INTEGRIN ALPHA M I DOMAIN Deposited 2002-08-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 144–335（192 aa） Fragment：I domain	Mutation：A318C	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.25 Å R-free 0.223
1N9Z INTEGRIN ALPHA M I DOMAIN MUTANT Deposited 2002-11-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 144–335（192 aa） Fragment：alpha M I domain	Mutation：C128A D132C K315C	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG 3000, sodium chloride, hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.50 Å R-free 0.278
1NA5 INTEGRIN ALPHA M I DOMAIN Deposited 2002-11-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 144–335（192 aa） Fragment：Alpha M I domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；298 K；PEG 8000, sodium chloride, potassium citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.50 Å R-free 0.228
2LKE Structures and Interaction Analyses of the Integrin Alpha-M Beta-2 Cytoplasmic Tails Deposited 2011-10-11	Different construct 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 1129–1152（24 aa） Fragment：C-terminal domain, UNP residues 1129-1152	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.6；308 K；Pressure ambient NMR sample composition 0.7 mM [1H] MYR-ALPHA-M-1, 200 mM [U-99% 2H] Dodecylphosphocholine-2, 10 mM sodium phosphate-3, 10 % [U-99% 2H] D2O-4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7 mM [1H] MYR-ALPHA-M-5, 200 mM [U-99% 2H] Dodecylphosphocholine-6, 10 mM sodium phosphate-7, 100 % [U-99% 2H] D2O-8, 100% D2O \| 100% D2O	Resolution not provided
2LKJ Structures and Interaction Analyses of the Integrin Alpha-M Beta-2 Cytoplasmic Tails Deposited 2011-10-12	Different construct Different mutation/modification 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 1129–1152（24 aa） Fragment：C-terminal domain, UNP residues 1129-1152	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.6；308 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.7 mM [1H] MYR-P-ALPHA-M-1, 200 mM [U-99% 2H] Dodecylphosphocholine-2, 10 mM sodium phosphate-3, 10 % [U-99% 2H] D2O-4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7 mM [1H] MYR-P-ALPHA-M-5, 200 mM [U-99% 2H] Dodecylphosphocholine-6, 10 mM sodium phosphate-7, 100 % [U-99% 2H] D2O-8, 100% D2O \| 100% D2O	Resolution not provided
3Q3G Crystal Structure of A-domain in complex with antibody Deposited 2010-12-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 148–337（190 aa） Fragment：UNP residues 148-337	Not recorded	EDO 1,2-ETHANEDIOL × 8 GOL GLYCEROL × 5 NA SODIUM ION × 1 CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；298 K；15% PEG4000, Tris pH 8.2, 0.3M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.244
3Q3G Crystal Structure of A-domain in complex with antibody Deposited 2010-12-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 148–337（190 aa） Fragment：UNP residues 148-337	Not recorded	EDO 1,2-ETHANEDIOL × 8 GOL GLYCEROL × 3 CA CALCIUM ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；298 K；15% PEG4000, Tris pH 8.2, 0.3M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.244
3Q3G Crystal Structure of A-domain in complex with antibody Deposited 2010-12-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 148–337（190 aa） Fragment：UNP residues 148-337	Not recorded	EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 2 CA CALCIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；298 K；15% PEG4000, Tris pH 8.2, 0.3M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.244
3Q3G Crystal Structure of A-domain in complex with antibody Deposited 2010-12-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 148–337（190 aa） Fragment：UNP residues 148-337	Not recorded	EDO 1,2-ETHANEDIOL × 8 GOL GLYCEROL × 3 CA CALCIUM ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；298 K；15% PEG4000, Tris pH 8.2, 0.3M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.244
3QA3 Crystal Structure of A-domain in complex with antibody Deposited 2011-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 148–337（190 aa） Fragment：UNP residues 148-337	Mutation：I316G	EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 3 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；298 K；13% PEG8000, Tris pH 8.2, 0.25M NaCl, 10mM CaCl2, 1mM PMSF, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.224
3QA3 Crystal Structure of A-domain in complex with antibody Deposited 2011-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 148–337（190 aa） Fragment：UNP residues 148-337	Mutation：I316G	GOL GLYCEROL × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；298 K；13% PEG8000, Tris pH 8.2, 0.25M NaCl, 10mM CaCl2, 1mM PMSF, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.224
3QA3 Crystal Structure of A-domain in complex with antibody Deposited 2011-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 148–337（190 aa） Fragment：UNP residues 148-337	Mutation：I316G	EDO 1,2-ETHANEDIOL × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；298 K；13% PEG8000, Tris pH 8.2, 0.25M NaCl, 10mM CaCl2, 1mM PMSF, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.224
3QA3 Crystal Structure of A-domain in complex with antibody Deposited 2011-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 148–337（190 aa） Fragment：UNP residues 148-337	Mutation：I316G	EDO 1,2-ETHANEDIOL × 3 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；298 K；13% PEG8000, Tris pH 8.2, 0.25M NaCl, 10mM CaCl2, 1mM PMSF, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.224
4M76 Integrin I domain of complement receptor 3 in complex with C3d Deposited 2013-08-12	Different construct 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 143–337（195 aa） Fragment：unp residues 143-337	Not recorded	NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 3350, pH 7, vapor diffusion, hanging drop, temperature 298K	Resolution 2.80 Å R-free 0.242
4XW2 Structural basis for simvastatin competitive antagonism of complement receptor 3 Deposited 2015-01-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 145–337（193 aa） Fragment：UNP residues 145-337	Not recorded	MG MAGNESIUM ION × 1 SIM Simvastatin acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2 M sodium malonate pH 7.0, 20% (w/v) PEG 3350	Resolution 2.00 Å R-free 0.232
6RHW Crystal structure of human CD11b I-domain (CD11b-I) in complex with Staphylococcus aureus octameric bi-component leukocidin LukGH Deposited 2019-04-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain C 143–337（195 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 24 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；Crystallization drops were prepared by mixing 1.0 uL LukGH/huCD11b-I complex (5.2 mg/mL) in 25 mM HEPES (pH 7.5), 1 mM MgCl2 with 0.5 uL reservoir solution containing 30% (v/v) Jeffamine-600 and 10% (v/v) DMSO.	Resolution 2.75 Å R-free 0.281
7AKK Structure of a complement factor-receptor complex Deposited 2020-10-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 143–337（195 aa） Chain H 143–337（195 aa）	Mutation：C128S,I316G Mutation：C128S,I316G	GOL GLYCEROL × 3 K POTASSIUM ION × 2 MG MAGNESIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；100 mM Tris-HCl (pH 8.0), 8% (w/v) polyethylene glycol (PEG) 8000	Resolution 3.40 Å R-free 0.229
7P2D Structure of alphaMbeta2/Cd11bCD18 headpiece in complex with a nanobody Deposited 2021-07-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 17–772（756 aa）	Not recorded	CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；1:1 ratio with reservoir containing 1.25 M sodium malonate, 76 mM HEPES pH 8.0, 24 mM HEPES pH 6.5, and 0.5% Jeffamine ED2001 pH 7.0	Resolution 3.20 Å R-free 0.295
7USL Integrin alphaM/beta2 ectodomain in complex with adenylate cyclase toxin RTX751 and M1F5 Fab Deposited 2022-04-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 17–1104（1088 aa）	Not recorded	CA CALCIUM ION × 33 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
7USM Integrin alphaM/beta2 ectodomain Deposited 2022-04-25	Different construct 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 A 17–1104（1088 aa）	Not recorded	CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8CE9 Crystal structure of human Cd11b I domain in C121 space group Deposited 2023-02-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 149–337（189 aa）	Not recorded	SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；25% PEG Smear Medium 0.1M cacodylate pH 5.5 0.2M ammonium sulfate	Resolution 2.11 Å R-free 0.239
8CE9 Crystal structure of human Cd11b I domain in C121 space group Deposited 2023-02-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 149–337（189 aa）	Not recorded	SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；25% PEG Smear Medium 0.1M cacodylate pH 5.5 0.2M ammonium sulfate	Resolution 2.11 Å R-free 0.239
8VOH HADDOCK models of human alphaM I-domain bound to the the N-terminal domain of the cytokine pleiotrophin Deposited 2024-01-15	Different construct 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 147–340（194 aa） Fragment：I-domain, residues 147-340	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure 1 NMR sample composition 0.2 mM [U-13C; U-15N] human alphaM I-domain, 1 mM The N-terminal domain of pleiotrophin, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-13C; U-15N] human alphaM I-domain, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-13C; U-15N] The N-terminal domain of pleiotrophin, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
8VOI HADDOCK models of active human alphaM I-domain bound to the the C-terminal domain of the cytokine pleiotrophin Deposited 2024-01-15	Different construct 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 148–331（184 aa） Fragment：I-domain, residues 148-331	Not recorded	MG MAGNESIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure 1 NMR sample composition 0.3 mM [U-100% 13C; U-100% 15N] active human alphaM I-domain, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] The C-terminal Domain of Pleiotrophin, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM The C-terminal Domain of Pleiotrophin, 0.2 mM [U-100% 13C; U-100% 15N; U-80% 2H] active human alphaM I-domain, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9GMU Structure ofhuman aM ligand binding domain in complex with the aCR3 nanobody Deposited 2024-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 145–337（193 aa） Fragment：UNP residues 145-337	Not recorded	MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；100 mM HEPES, pH 7.0, 1.5 M Li2S04.	Resolution 3.80 Å R-free 0.298
9GMU Structure ofhuman aM ligand binding domain in complex with the aCR3 nanobody Deposited 2024-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 145–337（193 aa） Fragment：UNP residues 145-337	Not recorded	MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；100 mM HEPES, pH 7.0, 1.5 M Li2S04.	Resolution 3.80 Å R-free 0.298
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 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 A 17–770（754 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
9RMA Cryo-EM structure of alphaM I-domain:C3d-anti-CR3-Nb complex focused refinement from the alphaM/beta2:C3d-anti-CR3-Nb headpiece complex Deposited 2025-06-18	Different construct 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 A 17–770（754 aa）	Not recorded	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 3.94 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 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 A 17–770（754 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 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 A 17–773（757 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 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 A 17–770（754 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 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 A 17–771（755 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

30 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ITAM_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–211； UniProt 149–337

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	8ce6
Deposition date deposition_date	2023-02-01
Structure title title	Crystal structure of human Cd11b I domain in P212121 space group
Keywords keywords	ITGAMA integrin leukocytes, 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	17.52 Å
Radius of gyration Rg (electron density) rg_electron	15.87 Å
Forward intensity I(0) i0	10583200.00
Molecular weight molecular_weight	23583.0 kDa
Excluded volume excluded_volume	29287 Å³
Envelope volume envelope_volume	32287 Å³
Hydration-shell volume shell_volume	16687 Å³
Envelope diameter envelope_diameter	53.4 Å
Shell Rg shell_rg	22.34 Å
Envelope Rg envelope_rg	16.15 Å
Shape Rg shape_rg	15.81 Å
Total Rg total_rg	17.07 Å
Total atoms total_atoms	3280
Residues n_residues	196
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	52.6 Å
Rg (real space) rg_real	17.36 Å
Rg uncertainty (real space) rg_real_error	0.20 Å
I(0) (real space) i0_real	1.0580e+07
I(0) uncertainty (real space) i0_real_error	1.1130e+05
Rg (reciprocal space) rg_reciprocal	17.38 Å
I(0) (reciprocal space) i0_reciprocal	10580000.0000
Solution quality estimate total_estimate	0.8997
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.014
Kurtosis Kurtosis kurtosis	-0.473
Angular range angular_range	— – 0.4550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2168000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.972

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Integrin alpha-M
Molecular weight formula_weight	24634.9 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	3478

MHHHHHHSSGVDLGTENLYFQSSDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKSLFSLMQYSEEFRIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVITDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVNNFEALKTIQNQLREKIFAIEGEPEA

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 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	88

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8. Citations (1)

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Unit-cell length a length_a	39.482 Å
Unit-cell length b length_b	50.906 Å
Unit-cell length c length_c	101.399 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	4

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

Resolution resolution	1.582 Å
Low-resolution limit resolution_low	50.700 Å
R factor r_factor	—
R_work r_work	0.1747
R_free r_free	0.2084

fit	/app/data/saxs_computation/ce/8ce6/8ce6.fit
pddf	/app/data/pr_computation/ce/8ce6/8ce6.pr.out
profile	/app/data/saxs_computation/ce/8ce6/8ce6.dat