7c7j

Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(G12V,Q63E)

Method: X-RAY DIFFRACTION D_max: 85.8 Å Quality: EXCELLENT

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

Ras-related protein Rap-1b

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 1–167	Mutation：G12V,Q63E	SH3 and multiple ankyrin repeat domains protein 3 × 1 （Q9BYB0） GTP GUANOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；10% (w/v) PEG 8000, 100 mM Imidazole/Hydrochloric acid (pH 8.0), 200 mM Calcium acetate	Resolution 2.39 Å R-free 0.255
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–167	Mutation：G12V,Q63E	SH3 and multiple ankyrin repeat domains protein 3 × 1 （Q9BYB0） GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；10% (w/v) PEG 8000, 100 mM Imidazole/Hydrochloric acid (pH 8.0), 200 mM Calcium acetate	Resolution 2.39 Å R-free 0.255

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 7C7J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3BRW Structure of the Rap-RapGAP complex Deposited 2007-12-21	Different construct Different mutation/modification 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 1–167（167 aa） Fragment：UNP residues 1-167	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；8-11% PEG 2000 MME, 100mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 3.40 Å R-free 0.280
3CF6 Structure of Epac2 in complex with cyclic-AMP and Rap Deposited 2008-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 1–167（167 aa） Fragment：UNP residues 1-167	Not recorded	SP1 6-(6-AMINO-PURIN-9-YL)-2-THIOXO-TETRAHYDRO-2-FURO[3,2-D][1,3,2]DIOXAPHOSPHININE-2,7-DIOL × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M Li2SO4, 0.1M citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.20 Å R-free 0.265
3CF6 Structure of Epac2 in complex with cyclic-AMP and Rap Deposited 2008-03-02	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 R 1–167（167 aa） Fragment：UNP residues 1-167	Not recorded	SP1 6-(6-AMINO-PURIN-9-YL)-2-THIOXO-TETRAHYDRO-2-FURO[3,2-D][1,3,2]DIOXAPHOSPHININE-2,7-DIOL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M Li2SO4, 0.1M citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.20 Å R-free 0.265
4DXA Co-crystal structure of Rap1 in complex with KRIT1 Deposited 2012-02-27	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–167（167 aa）	Mutation：G12V	GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.2M KNO3, 20% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.95 Å R-free 0.239
4HDO Crystal structure of the binary Complex of KRIT1 bound to the Rap1 GTPase Deposited 2012-10-02	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 1–167（167 aa） Fragment：UNP residues 1-167	Not recorded	GOL GLYCEROL × 1 MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；278 K；15% PEG2000 MME, 100 mM Tris, 100 mM potassium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K	Resolution 1.67 Å R-free 0.231
4HDQ Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and the Heart of Glass (HEG1) cytoplasmic tail Deposited 2012-10-02	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 B 1–167（167 aa） Fragment：UNP residues 1-167	Not recorded	GOL GLYCEROL × 1 MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；278 K；15% PEG2000 MME, 100 mM Tris, 100 mM potassium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K	Resolution 1.95 Å R-free 0.263
4M8N Crystal Structure of PlexinC1/Rap1B Complex Deposited 2013-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–166（166 aa） Chain H 1–166（166 aa）	Not recorded	MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 AF3 ALUMINUM FLUORIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；294.15 K；0.1 M HEPES, 5% 2-propanol, 25% PEG 3350, 3.6% polypropylene glycol P400, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K	Resolution 3.29 Å R-free 0.299
4M8N Crystal Structure of PlexinC1/Rap1B Complex Deposited 2013-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–166（166 aa） Chain G 1–166（166 aa）	Not recorded	MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 AF3 ALUMINUM FLUORIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；294.15 K；0.1 M HEPES, 5% 2-propanol, 25% PEG 3350, 3.6% polypropylene glycol P400, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K	Resolution 3.29 Å R-free 0.299
4MGI Selective activation of Epac1 and Epac2 Deposited 2013-08-28	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 R 1–167（167 aa） Fragment：UNP residues 1-169	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.271
4MGI Selective activation of Epac1 and Epac2 Deposited 2013-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 1–167（167 aa） Fragment：UNP residues 1-169	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.271
4MGK Selective activation of Epac1 and Epac2 Deposited 2013-08-28	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 R 1–167（167 aa） Fragment：UNP residues 1-169	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.264
4MGK Selective activation of Epac1 and Epac2 Deposited 2013-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 1–167（167 aa） Fragment：UNP residues 1-169	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.264
4MGY Selective activation of Epac1 and Epac2 Deposited 2013-08-29	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 R 1–167（167 aa） Fragment：UNP residues 1-169	Not recorded	H07 (2S,4aR,6R,7R,7aR)-6-{6-amino-8-[(4-chlorophenyl)sulfanyl]-9H-purin-9-yl}-7-methoxytetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-2-ol 2-oxide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.60 Å R-free 0.270
4MGY Selective activation of Epac1 and Epac2 Deposited 2013-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 1–167（167 aa） Fragment：UNP residues 1-169	Not recorded	H07 (2S,4aR,6R,7R,7aR)-6-{6-amino-8-[(4-chlorophenyl)sulfanyl]-9H-purin-9-yl}-7-methoxytetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-2-ol 2-oxide × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.60 Å R-free 0.270
4MGZ Selective activation of Epac1 and Epac2 Deposited 2013-08-29	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 R 1–167（167 aa） Fragment：UNP residues 1-169	Not recorded	HR6 (2S,4aR,6R,7R,7aS)-6-[6-amino-8-(benzylsulfanyl)-9H-purin-9-yl]-2-sulfanyltetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol 2-oxide × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.00 Å R-free 0.264
4MGZ Selective activation of Epac1 and Epac2 Deposited 2013-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 1–167（167 aa） Fragment：UNP residues 1-169	Not recorded	HR6 (2S,4aR,6R,7R,7aS)-6-[6-amino-8-(benzylsulfanyl)-9H-purin-9-yl]-2-sulfanyltetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol 2-oxide × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.00 Å R-free 0.264
4MH0 Selective activation of Epac1 and Epac2 Deposited 2013-08-29	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 R 1–167（167 aa） Fragment：UNP residues 1-169	Not recorded	HR4 (2S,4aR,6R,7R,7aS)-6-{6-amino-8-[(4-fluorobenzyl)sulfanyl]-9H-purin-9-yl}-2-sulfanyltetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol 2-oxide × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.40 Å R-free 0.282
4MH0 Selective activation of Epac1 and Epac2 Deposited 2013-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 1–167（167 aa） Fragment：UNP residues 1-169	Not recorded	HR4 (2S,4aR,6R,7R,7aS)-6-{6-amino-8-[(4-fluorobenzyl)sulfanyl]-9H-purin-9-yl}-2-sulfanyltetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol 2-oxide × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.40 Å R-free 0.282
5KHO Rasip1 RA domain in complex with Rap1B Deposited 2016-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–167（167 aa） Chain D 1–167（167 aa）	Not recorded	GOL GLYCEROL × 1 MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；16% PEG 8K, 200mM Calcium Acetate, and 100mM MES pH 6.5	Resolution 2.78 Å R-free 0.286
6AXF Structure of RasGRP2 in complex with Rap1B Deposited 2017-09-06	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 1–167（167 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；17% PEG3350 and 10 mM sodium citrate (pH 5.6)	Resolution 3.10 Å R-free 0.258
6AXF Structure of RasGRP2 in complex with Rap1B Deposited 2017-09-06	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 1–167（167 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；17% PEG3350 and 10 mM sodium citrate (pH 5.6)	Resolution 3.10 Å R-free 0.258
6AXF Structure of RasGRP2 in complex with Rap1B Deposited 2017-09-06	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 1–167（167 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；17% PEG3350 and 10 mM sodium citrate (pH 5.6)	Resolution 3.10 Å R-free 0.258
6AXF Structure of RasGRP2 in complex with Rap1B Deposited 2017-09-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–167（167 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；17% PEG3350 and 10 mM sodium citrate (pH 5.6)	Resolution 3.10 Å R-free 0.258
6AXF Structure of RasGRP2 in complex with Rap1B Deposited 2017-09-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 1–167（167 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；17% PEG3350 and 10 mM sodium citrate (pH 5.6)	Resolution 3.10 Å R-free 0.258
6AXF Structure of RasGRP2 in complex with Rap1B Deposited 2017-09-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–167（167 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；17% PEG3350 and 10 mM sodium citrate (pH 5.6)	Resolution 3.10 Å R-free 0.258
6AXF Structure of RasGRP2 in complex with Rap1B Deposited 2017-09-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 1–167（167 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；17% PEG3350 and 10 mM sodium citrate (pH 5.6)	Resolution 3.10 Å R-free 0.258
6AXF Structure of RasGRP2 in complex with Rap1B Deposited 2017-09-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 1–167（167 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；17% PEG3350 and 10 mM sodium citrate (pH 5.6)	Resolution 3.10 Å R-free 0.258
6BA6 Solution structure of Rap1b/talin complex Deposited 2017-10-12	Different mutation/modification 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 1–167（167 aa）	Mutation：G12V	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.6；301 K；Ionic strength (raw mmCIF value) 50mM NaCl, 5mM MgCl2；Pressure 101325 NMR measurement conditions pH 6.6；301 K；Ionic strength (raw mmCIF value) 50mM NaCl, 5mM MgCl2；Pressure 101325 NMR sample composition 0.6 mM [U-13C; U-15N] Rap1b, 0.9 mM talin-F0, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5 mM [U-13C; U-15N] talin-F0, 0.7 mM Rap1b, 95% H20, 5% D2O \| 95% H20, 5% D2O NMR sample composition 0.5 mM [U-15N; U-2H] talin-F0, 0.7 mM Rap1b, 95% H20, 5% D2O \| 95% H20, 5% D2O NMR sample composition 0.5 mM [U-13C; U-15N] talin-F0, 0.7 mM Rap1b, 0.2% H20, 99.8% D20 \| 0.2% H20, 99.8% D20 NMR sample composition 0.6 mM [U-13C; U-15N] Rap1b, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6KYK Crystal structure of Shank3 NTD-ANK mutant in complex with Rap1 Deposited 2019-09-19	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 C 1–167（167 aa） Chain D 1–167（167 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 1% Dextran sulfate sodium salt, 5% PEG 20000, 10% PEG 1500	Resolution 2.82 Å R-free 0.300
6KYK Crystal structure of Shank3 NTD-ANK mutant in complex with Rap1 Deposited 2019-09-19	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 1–167（167 aa） Chain F 1–167（167 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 1% Dextran sulfate sodium salt, 5% PEG 20000, 10% PEG 1500	Resolution 2.82 Å R-free 0.300
6OQ3 Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi2 Deposited 2019-04-25	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 1–167（167 aa）	Not recorded	7WO 2-hydroxynaphthalene-1-carbaldehyde × 1 MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20-25% PEG 3,350, 100 mM Tris, pH 8.5, 100 mM KCl	Resolution 1.85 Å R-free 0.292
6OQ4 Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi1 Deposited 2019-04-25	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 1–167（167 aa）	Not recorded	N0G 2-{(Z)-[(2-hydroxynaphthalen-1-yl)methylidene]amino}-N-[(1S)-1-phenylethyl]benzamide × 1 MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20-25% PEG 3,350, 100 mM Tris, pH 8.5, 100 mM KCl	Resolution 1.75 Å R-free 0.264
6UZK Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi6 Deposited 2019-11-15	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 1–167（167 aa）	Not recorded	QMA 2-hydroxy-6-methoxynaphthalene-1-carbaldehyde × 1 MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20-25% PEG 3,350, 100 mM Tris, pH 8.5, 100 mM KCl	Resolution 1.92 Å R-free 0.286
7C7I Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(E30D,K31E) Deposited 2020-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–167（167 aa） Chain B 1–167（167 aa）	Mutation：E30D,K31E Mutation：E30D,K31E	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；14.4% (w/v) PEG 8000, Sodium cacodylate/Hydrochloric acid (pH 6.5), 160 mM Calcium acetate, 20% (v/v) Glycerol	Resolution 2.28 Å R-free 0.246
8SU8 Co-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde derivative (6-(furan-2-yl)-2-hydroxy-1-naphthaldehyde). Deposited 2023-05-11	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 1–167（167 aa）	Not recorded	XE2 (6P)-6-(furan-2-yl)-2-hydroxynaphthalene-1-carbaldehyde × 1 MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% PEG 3350, 100 mM Tris, pH 8.5, 100 mM KCl	Resolution 2.01 Å R-free 0.238
8T09 Co-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde derivative (6-ethynyl-2-hydroxy-1-naphthaldehyde) Deposited 2023-05-31	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 1–167（167 aa）	Not recorded	XHZ 6-ethynyl-2-hydroxynaphthalene-1-carbaldehyde × 1 MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 3350, 100mM Tris, pH 8.5, 100 mM KCl	Resolution 2.15 Å R-free 0.247
8T7V Co-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde derivative (6-(furan-2-yl)-2-hydroxy-1-naphthaldehyde) Deposited 2023-06-21	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 1–167（167 aa）	Not recorded	ZTA (7M)-7-(furan-2-yl)-2-hydroxynaphthalene-1-carbaldehyde × 1 MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20% PEG 3350, 100mM Tris, pH 8.5, 100mM KCl	Resolution 2.25 Å R-free 0.250

22 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAP1B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–167； UniProt 1–167 Author chain B； PDBConstruct 1–167； UniProt 1–167

SH3 and multiple ankyrin repeat domains protein 3

Homo sapiens

UniProt Q9BYB0

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 C； UniProt 1–99	Not recorded	Ras-related protein Rap-1b × 1 （P61224） GTP GUANOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；10% (w/v) PEG 8000, 100 mM Imidazole/Hydrochloric acid (pH 8.0), 200 mM Calcium acetate	Resolution 2.39 Å R-free 0.255
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–99	Not recorded	Ras-related protein Rap-1b × 1 （P61224） GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；10% (w/v) PEG 8000, 100 mM Imidazole/Hydrochloric acid (pH 8.0), 200 mM Calcium acetate	Resolution 2.39 Å R-free 0.255

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7C7J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6CPK Solution structure of SH3 domain from Shank3 Deposited 2018-03-13	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 352–411（60 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 1 mM [U-99% 13C; U-99% 15N] Shank3 SH3, 20 mM Bis-Tris, 100 mM KCl, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-99% 13C; U-99% 15N] Shank3 SH3, 20 mM Bis-Tris, 100 mM KCl, 100% D2O \| 100% D2O NMR sample composition 1 mM [U-99% 15N] Shank3 SH3, 20 mM Bis-Tris, 100 mM KCl, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM Shank3 SH3, 20 mM Bis-Tris, 100 mM KCl, 100% D2O \| 100% D2O	Resolution not provided
7C7I Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(E30D,K31E) Deposited 2020-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–99（99 aa） Chain D 1–99（99 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；14.4% (w/v) PEG 8000, Sodium cacodylate/Hydrochloric acid (pH 6.5), 160 mM Calcium acetate, 20% (v/v) Glycerol	Resolution 2.28 Å R-free 0.246

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

View Construct and Data Evidence

UniProt name	SHAN3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–99； UniProt 1–99 Author chain D； PDBConstruct 1–99； UniProt 1–99

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	7c7j
Deposition date deposition_date	2020-05-25
Structure title title	Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(G12V,Q63E)
Keywords keywords	SHANK3, Rap1b, SPN, Ras, 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	27.25 Å
Radius of gyration Rg (electron density) rg_electron	26.50 Å
Forward intensity I(0) i0	59401200.00
Molecular weight molecular_weight	59112.0 kDa
Excluded volume excluded_volume	73548 Å³
Envelope volume envelope_volume	93282 Å³
Hydration-shell volume shell_volume	29553 Å³
Envelope diameter envelope_diameter	86.0 Å
Shell Rg shell_rg	33.69 Å
Envelope Rg envelope_rg	26.62 Å
Shape Rg shape_rg	26.53 Å
Total Rg total_rg	27.13 Å
Total atoms total_atoms	4144
Residues n_residues	511
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	85.8 Å
Rg (real space) rg_real	27.23 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	5.9400e+07
I(0) uncertainty (real space) i0_real_error	8.6010e+05
Rg (reciprocal space) rg_reciprocal	27.24 Å
I(0) (reciprocal space) i0_reciprocal	59400000.0000
Solution quality estimate total_estimate	0.9048
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	29.6 Å
Skewness Skewness skewness	0.292
Kurtosis Kurtosis kurtosis	-0.504
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10730000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.944

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Ras-related protein Rap-1b
Molecular weight formula_weight	19063.6 kDa
Mutation mutation	G12V,Q63E
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4235

MREYKLVVLGSVGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEEFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR

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	SH3 and multiple ankyrin repeat domains protein 3
Molecular weight formula_weight	11193.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MDGPGASAVVVRVGIPDLQQTKCLRLDPAAPVWAAKQRVLCALNHSLQDALNYGLFQPPSRGRAGKFLDEERLLQEYPPNLDTPLPYLEFRYKRRVYAQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	91

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d7c7ja_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d7c7jb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

CATH v4.4 (4 domains)

Domain ID domain_id	7c7jA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7c7jB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7c7jC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	7c7jD01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (3)

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Unit-cell length a length_a	58.215 Å
Unit-cell length b length_b	191.926 Å
Unit-cell length c length_c	48.876 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.390 Å
Low-resolution limit resolution_low	47.980 Å
R factor r_factor	0.1889
R_work r_work	0.1854
R_free r_free	0.2552

fit	/app/data/saxs_computation/c7/7c7j/7c7j.fit
pddf	/app/data/pr_computation/c7/7c7j/7c7j.pr.out
profile	/app/data/saxs_computation/c7/7c7j/7c7j.dat

Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(G12V,Q63E)

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

Ras-related protein Rap-1b

State in the Current Structure

Other States of the Same Protein in the Database

SH3 and multiple ankyrin repeat domains protein 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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)