3u23

Atomic resolution crystal structure of the 2nd SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide from human RIN3

Method: X-RAY DIFFRACTION D_max: 41.5 Å Quality: GOOD

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

CD2-associated protein

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 109–168	Fragment：unp residues 109-168	Ras and Rab interactor 3 × 1 （Q8TB24） EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 1.4 M tri-sodium citrate dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.11 Å R-free 0.167

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 3U23	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2FEI Solution structure of the second SH3 domain of Human CMS protein Deposited 2005-12-15	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 111–166（56 aa） Fragment：The second SH3 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.85；295 K；Pressure 1 NMR sample composition 1.0-2.0mM 15N, 13C-labeled CMS SH3 domain, 20mM phosphate buffer (pH 6.85), 50mM sodium chloride, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0-2.0mM 15N, 13C-labeled CMS SH3 domain, 20mM phosphate buffer (pH 6.85), 50mM sodium chloride, 100% D2O \| 100% D2O	Resolution not provided
2J6F N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) BOUND TO CBL-B PEPTIDE Deposited 2006-09-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–62（62 aa） Fragment：SH3, RESIDUES 1-62	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；20% PEG3000, 0.1M ACETATE PH 5.5	Resolution 1.70 Å R-free 0.218
2J6K N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) Deposited 2006-09-29	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 1–62（62 aa） Fragment：SH3, RESIDUES 1-62	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；0.1 M SODIUM CITRATE PH 6.1, 25% PEG 4000, 20% ISOPROPANOL	Resolution 2.77 Å R-free 0.274
2J6K N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) Deposited 2006-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain J 1–62（62 aa） Fragment：SH3, RESIDUES 1-62	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；0.1 M SODIUM CITRATE PH 6.1, 25% PEG 4000, 20% ISOPROPANOL	Resolution 2.77 Å R-free 0.274
2J6K N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) Deposited 2006-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain K 1–62（62 aa） Fragment：SH3, RESIDUES 1-62	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；0.1 M SODIUM CITRATE PH 6.1, 25% PEG 4000, 20% ISOPROPANOL	Resolution 2.77 Å R-free 0.274
2J6K N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) Deposited 2006-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain L 1–62（62 aa） Fragment：SH3, RESIDUES 1-62	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；0.1 M SODIUM CITRATE PH 6.1, 25% PEG 4000, 20% ISOPROPANOL	Resolution 2.77 Å R-free 0.274
2J6K N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) Deposited 2006-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–62（62 aa） Fragment：SH3, RESIDUES 1-62	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；0.1 M SODIUM CITRATE PH 6.1, 25% PEG 4000, 20% ISOPROPANOL	Resolution 2.77 Å R-free 0.274
2J6K N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) Deposited 2006-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–62（62 aa） Fragment：SH3, RESIDUES 1-62	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；0.1 M SODIUM CITRATE PH 6.1, 25% PEG 4000, 20% ISOPROPANOL	Resolution 2.77 Å R-free 0.274
2J6K N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) Deposited 2006-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–62（62 aa） Fragment：SH3, RESIDUES 1-62	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；0.1 M SODIUM CITRATE PH 6.1, 25% PEG 4000, 20% ISOPROPANOL	Resolution 2.77 Å R-free 0.274
2J6K N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) Deposited 2006-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–62（62 aa） Fragment：SH3, RESIDUES 1-62	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；0.1 M SODIUM CITRATE PH 6.1, 25% PEG 4000, 20% ISOPROPANOL	Resolution 2.77 Å R-free 0.274
2J6K N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) Deposited 2006-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 1–62（62 aa） Fragment：SH3, RESIDUES 1-62	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；0.1 M SODIUM CITRATE PH 6.1, 25% PEG 4000, 20% ISOPROPANOL	Resolution 2.77 Å R-free 0.274
2J6K N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) Deposited 2006-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 1–62（62 aa） Fragment：SH3, RESIDUES 1-62	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；0.1 M SODIUM CITRATE PH 6.1, 25% PEG 4000, 20% ISOPROPANOL	Resolution 2.77 Å R-free 0.274
2J6K N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) Deposited 2006-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 1–62（62 aa） Fragment：SH3, RESIDUES 1-62	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；0.1 M SODIUM CITRATE PH 6.1, 25% PEG 4000, 20% ISOPROPANOL	Resolution 2.77 Å R-free 0.274
2J6K N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) Deposited 2006-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 1–62（62 aa） Fragment：SH3, RESIDUES 1-62	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；0.1 M SODIUM CITRATE PH 6.1, 25% PEG 4000, 20% ISOPROPANOL	Resolution 2.77 Å R-free 0.274
2J6O ATYPICAL POLYPROLINE RECOGNITION BY THE CMS N-TERMINAL SH3 DOMAIN. CMS:CD2 HETEROTRIMER Deposited 2006-10-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–62（62 aa） Fragment：SH3 DOMAIN, RESIDUES 1-62	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；20% PEG3000, 0.1M ACETATE PH 5.5	Resolution 2.23 Å R-free 0.286
2J7I ATYPICAL POLYPROLINE RECOGNITION BY THE CMS N-TERMINAL SH3 DOMAIN. CMS:CD2 HETERODIMER Deposited 2006-10-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–62（62 aa） Fragment：SH3 DOMAIN, RESIDUES 1-62	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；30% PEG8000, 0.2M NACL, 0.1M TRIS-HCL PH 8.0	Resolution 2.90 Å R-free 0.295
2J7I ATYPICAL POLYPROLINE RECOGNITION BY THE CMS N-TERMINAL SH3 DOMAIN. CMS:CD2 HETERODIMER Deposited 2006-10-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–62（62 aa） Fragment：SH3 DOMAIN, RESIDUES 1-62	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；30% PEG8000, 0.2M NACL, 0.1M TRIS-HCL PH 8.0	Resolution 2.90 Å R-free 0.295
3AA6 Crystal structure of Actin capping protein in complex with the Cp-binding motif derived from CD2AP Deposited 2009-11-11	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 C 485–507（23 aa） Fragment：recidues 485-507	Not recorded	BA BARIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；10% PEG 400, 20MM BACL2, 100MM MES-NAOH, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.90 Å R-free 0.238
3LK4 Crystal structure of CapZ bound to the uncapping motif from CD2AP Deposited 2010-01-27	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 C 475–503（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.99 Å R-free 0.272
3LK4 Crystal structure of CapZ bound to the uncapping motif from CD2AP Deposited 2010-01-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain 3 475–503（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.99 Å R-free 0.272
3LK4 Crystal structure of CapZ bound to the uncapping motif from CD2AP Deposited 2010-01-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain 6 475–503（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.99 Å R-free 0.272
3LK4 Crystal structure of CapZ bound to the uncapping motif from CD2AP Deposited 2010-01-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain 9 475–503（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.99 Å R-free 0.272
3LK4 Crystal structure of CapZ bound to the uncapping motif from CD2AP Deposited 2010-01-27	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 F 475–503（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.99 Å R-free 0.272
3LK4 Crystal structure of CapZ bound to the uncapping motif from CD2AP Deposited 2010-01-27	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 475–503（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.99 Å R-free 0.272
3LK4 Crystal structure of CapZ bound to the uncapping motif from CD2AP Deposited 2010-01-27	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 475–503（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.99 Å R-free 0.272
3LK4 Crystal structure of CapZ bound to the uncapping motif from CD2AP Deposited 2010-01-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain O 475–503（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.99 Å R-free 0.272
3LK4 Crystal structure of CapZ bound to the uncapping motif from CD2AP Deposited 2010-01-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain R 475–503（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.99 Å R-free 0.272
3LK4 Crystal structure of CapZ bound to the uncapping motif from CD2AP Deposited 2010-01-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain U 475–503（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.99 Å R-free 0.272
3LK4 Crystal structure of CapZ bound to the uncapping motif from CD2AP Deposited 2010-01-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain X 475–503（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.99 Å R-free 0.272
3LK4 Crystal structure of CapZ bound to the uncapping motif from CD2AP Deposited 2010-01-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain 0 475–503（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.99 Å R-free 0.272
4WCI Crystal structure of the 1st SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide (aa 378-393) from human RIN3 Deposited 2014-09-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–60（60 aa） Fragment：UNP residues 1-60	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Ca(ac) pH 4.2, 0.2 M Li2SO4 and 25% PEG 10 000	Resolution 1.65 Å R-free 0.219
4WCI Crystal structure of the 1st SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide (aa 378-393) from human RIN3 Deposited 2014-09-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–60（60 aa） Fragment：UNP residues 1-60	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Ca(ac) pH 4.2, 0.2 M Li2SO4 and 25% PEG 10 000	Resolution 1.65 Å R-free 0.219
4WCI Crystal structure of the 1st SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide (aa 378-393) from human RIN3 Deposited 2014-09-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–60（60 aa） Fragment：UNP residues 1-60	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Ca(ac) pH 4.2, 0.2 M Li2SO4 and 25% PEG 10 000	Resolution 1.65 Å R-free 0.219
4X1V Crystal structure of the 2nd SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide (aa 76-91) from human ARAP1 Deposited 2014-11-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 109–168（60 aa） Fragment：UNP residues 109-168	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 1.4 M tri-sodium citrate dehydrate	Resolution 1.58 Å R-free 0.200
7DS6 Crystal structure of actin capping protein in complex with twinflin-1/CD2AP CPI chimera peptide (TWN-CDC) Deposited 2020-12-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 496–507（12 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；5% (w/v) PEG 3350, 5% (v/v) ethanol, 50mM Tris-HCl (pH = 7.0)	Resolution 1.69 Å R-free 0.253
7DS8 Crystal structure of actin capping protein in complex with twinflin-1/CD2AP CPI chimera peptide (CDN-TWC) Deposited 2020-12-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 485–493（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；4% (w/v) PEG 3350, 50mM Tris-HCl (pH = 7.0)	Resolution 1.95 Å R-free 0.233

11 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CD2AP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–65； UniProt 109–168

Ras and Rab interactor 3

OrganismNot specified

UniProt Q8TB24

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 452–467	Fragment：unp residues 452-467 Non-standard monomer：Yes (specific site not provided by mmCIF)	CD2-associated protein × 1 （Q9Y5K6） EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 1.4 M tri-sodium citrate dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.11 Å R-free 0.167

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3U23	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4WCI Crystal structure of the 1st SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide (aa 378-393) from human RIN3 Deposited 2014-09-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 378–393（16 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Ca(ac) pH 4.2, 0.2 M Li2SO4 and 25% PEG 10 000	Resolution 1.65 Å R-free 0.219
4WCI Crystal structure of the 1st SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide (aa 378-393) from human RIN3 Deposited 2014-09-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 378–393（16 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Ca(ac) pH 4.2, 0.2 M Li2SO4 and 25% PEG 10 000	Resolution 1.65 Å R-free 0.219
4WCI Crystal structure of the 1st SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide (aa 378-393) from human RIN3 Deposited 2014-09-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 378–393（16 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Ca(ac) pH 4.2, 0.2 M Li2SO4 and 25% PEG 10 000	Resolution 1.65 Å R-free 0.219

1 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RIN3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–16； UniProt 452–467

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	3u23
Deposition date deposition_date	2011-09-30
Structure title title	Atomic resolution crystal structure of the 2nd SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide from human RIN3
Keywords keywords	Structural Genomics, Structural Genomics Consortium, SGC, Beta-barrel, Adaptor protein, Protein binding; PROTEIN BINDING
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	12.66 Å
Radius of gyration Rg (electron density) rg_electron	11.17 Å
Forward intensity I(0) i0	1382830.00
Molecular weight molecular_weight	8006.0 kDa
Excluded volume excluded_volume	10116 Å³
Envelope volume envelope_volume	11265 Å³
Hydration-shell volume shell_volume	8677 Å³
Envelope diameter envelope_diameter	39.3 Å
Shell Rg shell_rg	16.79 Å
Envelope Rg envelope_rg	11.67 Å
Shape Rg shape_rg	11.13 Å
Total Rg total_rg	12.82 Å
Total atoms total_atoms	566
Residues n_residues	69
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	41.5 Å
Rg (real space) rg_real	12.58 Å
Rg uncertainty (real space) rg_real_error	0.22 Å
I(0) (real space) i0_real	1.3830e+06
I(0) uncertainty (real space) i0_real_error	1.3750e+04
Rg (reciprocal space) rg_reciprocal	12.58 Å
I(0) (reciprocal space) i0_reciprocal	1383000.0000
Solution quality estimate total_estimate	0.8737
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.7 Å
Skewness Skewness skewness	0.177
Kurtosis Kurtosis kurtosis	-0.240
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	599000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.791; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.984

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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	CD2-associated protein
Molecular weight formula_weight	7444.4 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	687

GPLGSKKRQCKVLFEYIPQNEDELELKVGDIIDINEEVEEGWWSGTLNNKLGLFPSNFVKELEVT

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	Ras and Rab interactor 3
Molecular weight formula_weight	1803.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

TAKQPPVPPPRKKRISX

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	86

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3u23A00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

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8. Citations (1)

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Unit-cell length a length_a	53.130 Å
Unit-cell length b length_b	32.040 Å
Unit-cell length c length_c	39.180 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.56 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.110 Å
Low-resolution limit resolution_low	27.430 Å
R factor r_factor	0.1515
R_work r_work	0.1507
R_free r_free	0.1666

fit	/app/data/saxs_computation/u2/3u23/3u23.fit
pddf	/app/data/pr_computation/u2/3u23/3u23.pr.out
profile	/app/data/saxs_computation/u2/3u23/3u23.dat

Atomic resolution crystal structure of the 2nd SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide from human RIN3

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

CD2-associated protein

State in the Current Structure

Other States of the Same Protein in the Database

Ras and Rab interactor 3

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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)