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8voi

HADDOCK models of active human alphaM I-domain bound to the the C-terminal domain of the cytokine pleiotrophin

Method: SOLUTION NMR Dmax: 73.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Integrin alpha-M

Homo sapiens

UniProt P11215

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 148–331 Fragment：I-domain, residues 148-331 Pleiotrophin × 1 （P21246） 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

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 8VOI 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 method 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 method 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 method 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 oligomeric state Different experimental method 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 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 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 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 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 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 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 oligomeric state Different experimental method 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 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 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 oligomeric state Different ligand/ion Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental conditions 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 ligand/ion Different experimental method 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 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 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 method 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 method 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 method 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
8CE6 Crystal structure of human Cd11b I domain in P212121 space group Deposited 2023-02-01 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 149–337（189 aa）
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
8CE9 Crystal structure of human Cd11b I domain in C121 space group Deposited 2023-02-01 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 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental conditions 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
9GMU Structure ofhuman aM ligand binding domain in complex with the aCR3 nanobody Deposited 2024-08-29 Different construct 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 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 ligand/ion Different experimental method 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 1–184； UniProt 148–331

Pleiotrophin

Homo sapiens

UniProt P21246

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 90–146 Fragment：C-terminal domain, residues 90-146 Integrin alpha-M × 1 （P11215） 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

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 8VOI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2N6F Structure of Pleiotrophin Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 33–168（136 aa） Fragment：UNP residues 33-168
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient
NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] PTN, 10 % v/v D2O, 10 mM MES, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
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 ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 33–90（58 aa） Fragment：N-terminal domain, residues 33-90
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

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PTN_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–57； UniProt 90–146

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

SAXS profile for 8voi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8voi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8voi
Deposition date deposition_date2024-01-15
Structure title titleHADDOCK models of active human alphaM I-domain bound to the the C-terminal domain of the cytokine pleiotrophin
Keywords keywordsintegrin, Mac-1, pleiotrophin, CELL ADHESION; CELL ADHESION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.04 Å
Radius of gyration Rg (electron density) rg_electron21.03 Å
Forward intensity I(0) i01052150000.00
Molecular weight molecular_weight275780.0 kDa
Excluded volume excluded_volume346350 ų
Envelope volume envelope_volume69541 ų
Hydration-shell volume shell_volume24460 ų
Envelope diameter envelope_diameter81.6 Å
Shell Rg shell_rg30.93 Å
Envelope Rg envelope_rg26.10 Å
Shape Rg shape_rg20.97 Å
Total Rg total_rg21.44 Å
Total atoms total_atoms39070
Residues n_residues2410
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax73.0 Å
Rg (real space) rg_real21.25 Å
Rg uncertainty (real space) rg_real_error0.67 Å
I(0) (real space) i0_real1.0520e+09
I(0) uncertainty (real space) i0_real_error1.6100e+07
Rg (reciprocal space) rg_reciprocal21.21 Å
I(0) (reciprocal space) i0_reciprocal1052000000.0000
Solution quality estimate total_estimate0.7313
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.3 Å
Skewness Skewness skewness0.668
Kurtosis Kurtosis kurtosis0.099
Angular range angular_range— – 0.3800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2261000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.544; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.874; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)