4dxa

Co-crystal structure of Rap1 in complex with KRIT1

Method: X-RAY DIFFRACTION D_max: 85.6 Å Quality: GOOD

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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	Krev interaction trapped protein 1 × 1 （O00522） 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

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 4DXA	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
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 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
7C7J Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(G12V,Q63E) Deposited 2020-05-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–167（167 aa）	Mutation：G12V,Q63E	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
7C7J Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(G12V,Q63E) Deposited 2020-05-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–167（167 aa）	Mutation：G12V,Q63E	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
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 38 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 3–169； UniProt 1–167

Krev interaction trapped protein 1

Homo sapiens

UniProt O00522

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 420–736	Fragment：FERM domain	Ras-related protein Rap-1b × 1 （P61224） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4DXA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3U7D Crystal structure of the KRIT1/CCM1 FERM domain in complex with the heart of glass (HEG1) cytoplasmic tail Deposited 2011-10-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 417–736（320 aa） Fragment：FERM domain, residues 417-736	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；10% PEG 4000 and 100mM Citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.49 Å R-free 0.309
3U7D Crystal structure of the KRIT1/CCM1 FERM domain in complex with the heart of glass (HEG1) cytoplasmic tail Deposited 2011-10-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 417–736（320 aa） Fragment：FERM domain, residues 417-736	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；10% PEG 4000 and 100mM Citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.49 Å R-free 0.309
4DX8 ICAP1 in complex with KRIT1 N-terminus Deposited 2012-02-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 1–198（198 aa） Fragment：Nudix domain	Not recorded	BR BROMIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.06M AmSO4, 0.2M Ammonium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.54 Å R-free 0.252
4DX8 ICAP1 in complex with KRIT1 N-terminus Deposited 2012-02-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–198（198 aa） Fragment：Nudix domain	Not recorded	BR BROMIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.06M AmSO4, 0.2M Ammonium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.54 Å R-free 0.252
4DX8 ICAP1 in complex with KRIT1 N-terminus Deposited 2012-02-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 1–198（198 aa） Fragment：Nudix domain	Not recorded	BR BROMIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.06M AmSO4, 0.2M Ammonium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.54 Å R-free 0.252
4DX8 ICAP1 in complex with KRIT1 N-terminus Deposited 2012-02-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 1–198（198 aa） Fragment：Nudix domain	Not recorded	BR BROMIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.06M AmSO4, 0.2M Ammonium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.54 Å R-free 0.252
4HDO Crystal structure of the binary Complex of KRIT1 bound to the Rap1 GTPase Deposited 2012-10-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 417–736（320 aa） Fragment：FERM domain (UNP residues 417-736)	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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 417–736（320 aa） Fragment：FERM domain (UNP residues 417-736)	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
4JIF Co-crystal structure of ICAP1 PTB domain in complex with a KRIT1 peptide Deposited 2013-03-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 170–198（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；18-20%PEG3350, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.226
4JIF Co-crystal structure of ICAP1 PTB domain in complex with a KRIT1 peptide Deposited 2013-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 170–198（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；18-20%PEG3350, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.226
4TKN Structure of the SNX17 FERM domain bound to the second NPxF motif of KRIT1 Deposited 2014-05-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 225–237（13 aa） Fragment：UNP residues 225-237	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.9 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 5% PEG 400	Resolution 3.00 Å R-free 0.268
4TKN Structure of the SNX17 FERM domain bound to the second NPxF motif of KRIT1 Deposited 2014-05-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 225–237（13 aa） Fragment：UNP residues 225-237	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.9 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 5% PEG 400	Resolution 3.00 Å R-free 0.268
4TKN Structure of the SNX17 FERM domain bound to the second NPxF motif of KRIT1 Deposited 2014-05-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 225–237（13 aa） Fragment：UNP residues 225-237	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.9 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 5% PEG 400	Resolution 3.00 Å R-free 0.268
5D68 Crystal structure of KRIT1 ARD-FERM Deposited 2015-08-11	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 52–529（478 aa） Fragment：ARD-FERM domain (UNP residues 52-529)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；0.05 M HEPES, pH 7.3, 8% ethylene glycol, 8% PEG8000	Resolution 2.91 Å R-free 0.246
5D68 Crystal structure of KRIT1 ARD-FERM Deposited 2015-08-11	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 52–529（478 aa） Fragment：ARD-FERM domain (UNP residues 52-529)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；0.05 M HEPES, pH 7.3, 8% ethylene glycol, 8% PEG8000	Resolution 2.91 Å R-free 0.246
5D68 Crystal structure of KRIT1 ARD-FERM Deposited 2015-08-11	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 52–529（478 aa） Fragment：ARD-FERM domain (UNP residues 52-529)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；0.05 M HEPES, pH 7.3, 8% ethylene glycol, 8% PEG8000	Resolution 2.91 Å R-free 0.246
6OQ3 Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi2 Deposited 2019-04-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 417–736（320 aa） Fragment：FERM domain	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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 417–736（320 aa） Fragment：FERM domain	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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 417–736（320 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
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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 419–736（318 aa） Fragment：FERM domain	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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 419–736（318 aa） Fragment：FERM domain	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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 417–736（320 aa） Fragment：FERM domain	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
9PVG Co-crystal structure of two CCM2 PTB domains bound to a KRIT1 peptide encompassing NPxF2 and NPxF3 Deposited 2025-08-01	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 E 227–255（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M TrisHCl pH 7, 20% PEG3350	Resolution 3.00 Å R-free 0.297
9PVG Co-crystal structure of two CCM2 PTB domains bound to a KRIT1 peptide encompassing NPxF2 and NPxF3 Deposited 2025-08-01	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 227–255（29 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M TrisHCl pH 7, 20% PEG3350	Resolution 3.00 Å R-free 0.297

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

View Construct and Data Evidence

UniProt name	KRIT1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–322； UniProt 420–736

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	4dxa
Deposition date deposition_date	2012-02-27
Structure title title	Co-crystal structure of Rap1 in complex with KRIT1
Keywords keywords	GTPase, FERM, Protein-protein interaction, GTP binding, Cytoplasmic, 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	25.78 Å
Radius of gyration Rg (electron density) rg_electron	24.72 Å
Forward intensity I(0) i0	48778900.00
Molecular weight molecular_weight	54860.0 kDa
Excluded volume excluded_volume	69007 Å³
Envelope volume envelope_volume	83163 Å³
Hydration-shell volume shell_volume	28306 Å³
Envelope diameter envelope_diameter	88.4 Å
Shell Rg shell_rg	31.70 Å
Envelope Rg envelope_rg	24.73 Å
Shape Rg shape_rg	24.71 Å
Total Rg total_rg	25.54 Å
Total atoms total_atoms	3851
Residues n_residues	470
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	85.6 Å
Rg (real space) rg_real	25.77 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	4.8780e+07
I(0) uncertainty (real space) i0_real_error	7.1920e+05
Rg (reciprocal space) rg_reciprocal	25.77 Å
I(0) (reciprocal space) i0_reciprocal	48780000.0000
Solution quality estimate total_estimate	0.8852
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	84.2 Å
Skewness Skewness skewness	0.361
Kurtosis Kurtosis kurtosis	-0.222
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10920000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.972

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Ras-related protein Rap-1b
Molecular weight formula_weight	19206.7 kDa
EC 编号 ec_number	3.6.5.2
Mutation mutation	G12V
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	4185

GSMREYKLVVLGSVGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR

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	Krev interaction trapped protein 1
Molecular weight formula_weight	37372.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSPEFEKVRIYRMDGSYRSVELKHGNNTTVQQIMEGMRLSQETQQYFTIWICSENLSLQLKPYHKPLQHVRDWPEILAELTNLDPQRETPQLFLRRDVRLPLEVEKQIEDPLAILILFDEARYNLLKGFYTAPDAKLITLASLLLQIVYGNYESKKHKQGFLNEENLKSIVPVTKLKSKAPHWTNRILHEYKNLSTSEGVSKEMHHLQRMFLQNCWEIPTYGAAFFTGQIFTKASPSNHKVIPVYVGVNIKGLHLLNMETKALLISLKYGCFMWQLGDTDTCFQIHSMENKMSFIVHTKQAGLVVKLLMKLNGQLMPTERNS

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	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
Molecular weight formula_weight	539.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	327

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4dxaa1
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	d4dxaa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	4dxaA00
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	4dxaB01
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	4dxaB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4dxaB03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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8. Citations (1)

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Unit-cell length a length_a	57.548 Å
Unit-cell length b length_b	77.970 Å
Unit-cell length c length_c	59.757 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.93 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	47.425 Å
R factor r_factor	0.1983
R_work r_work	0.1961
R_free r_free	0.2388

fit	/app/data/saxs_computation/dx/4dxa/4dxa.fit
pddf	/app/data/pr_computation/dx/4dxa/4dxa.pr.out
profile	/app/data/saxs_computation/dx/4dxa/4dxa.dat

Co-crystal structure of Rap1 in complex with KRIT1

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

Krev interaction trapped protein 1

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 (5)

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 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)