SAXSdb — 9pvg

▼

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

Malcavernin

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 51–228 Chain D； UniProt 51–228	Fragment：PTB domain (UNP residues 51-228)	Krev interaction trapped protein 1 × 1 （O00522）	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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 51–228 Chain C； UniProt 51–228	Fragment：PTB domain (UNP residues 51-228)	Krev interaction trapped protein 1 × 1 （O00522）	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

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 9PVG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4FQN Crystal structure of the CCM2 C-terminal Harmonin Homology Domain (HHD) Deposited 2012-06-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 283–379（97 aa） Fragment：C-terminal domain (unp residues 283-379) Chain B 283–379（97 aa） Fragment：C-terminal domain (unp residues 283-379)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；2.072M ammonium sulfate, 0.2M potassium formate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.219
4FQN Crystal structure of the CCM2 C-terminal Harmonin Homology Domain (HHD) Deposited 2012-06-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 283–379（97 aa） Fragment：C-terminal domain (unp residues 283-379)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；2.072M ammonium sulfate, 0.2M potassium formate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.219
4FQN Crystal structure of the CCM2 C-terminal Harmonin Homology Domain (HHD) Deposited 2012-06-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 283–379（97 aa） Fragment：C-terminal domain (unp residues 283-379)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；2.072M ammonium sulfate, 0.2M potassium formate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.219
4TVQ CCM3 in complex with CCM2 LD-like motif Deposited 2014-06-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 224–239（16 aa） Fragment：INTERDOMAIN LINKER LD-LIKE MOTIF RESIDUES 224-239	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；15-20% PEG3350, 0.1-0.2M POTASSIUM FLUORIDE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K	Resolution 2.80 Å R-free 0.277
4WJ7 CCM2 PTB domain in complex with KRIT1 NPxY/F3 Deposited 2014-09-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 51–228（178 aa） Fragment：PTB domain (UNP residues 51-228)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% (w/v) PEG 6000, 0.1M HEPES	Resolution 2.75 Å R-free 0.251
4WJ7 CCM2 PTB domain in complex with KRIT1 NPxY/F3 Deposited 2014-09-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 51–228（178 aa） Fragment：PTB domain (UNP residues 51-228)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% (w/v) PEG 6000, 0.1M HEPES	Resolution 2.75 Å R-free 0.251
4WJ7 CCM2 PTB domain in complex with KRIT1 NPxY/F3 Deposited 2014-09-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 51–228（178 aa） Fragment：PTB domain (UNP residues 51-228)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% (w/v) PEG 6000, 0.1M HEPES	Resolution 2.75 Å R-free 0.251
4WJ7 CCM2 PTB domain in complex with KRIT1 NPxY/F3 Deposited 2014-09-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 51–228（178 aa） Fragment：PTB domain (UNP residues 51-228)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% (w/v) PEG 6000, 0.1M HEPES	Resolution 2.75 Å R-free 0.251
4Y5O CCM2 HHD in complex with MEKK3 NPB1 Deposited 2015-02-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 304–400（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M potassium phosphate and 20% PEG 3350	Resolution 2.35 Å R-free 0.232
4YKC Crystal structure of cerebral cavernous malformation 2 C-terminal adaptor domain Deposited 2015-03-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 290–444（155 aa） Fragment：C-terminal adaptor domain, UNP residues 290-444	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；45% Tacsimate	Resolution 2.70 Å R-free 0.267
4YKD Crystal structure of truncated cerebral cavernous malformation 2 C-terminal adaptor domain Deposited 2015-03-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 290–376（87 aa） Fragment：truncated fragment of C-terminal adaptor domain, UNP residues 290-376	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Bis-Tris, 30%(w/v) polyethylene glycol 550, 50 mM calcium chloride	Resolution 1.93 Å R-free 0.235
4YL6 Crystal structure of truncated cerebral cavernous malformation 2 C-terminal adaptor domain in complex with an internal helix of mitogen-activated protein kinase kinase kinase 3 Deposited 2015-03-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 290–376（87 aa） Fragment：truncated fragment of C-terminal adaptor domain, UNP residues 290-376	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；3.5 M Sodium Formate	Resolution 2.10 Å R-free 0.237

7 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CCM2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–180； UniProt 51–228 Author chain B； PDBConstruct 3–180； UniProt 51–228 Author chain C； PDBConstruct 3–180； UniProt 51–228 Author chain D； PDBConstruct 3–180； UniProt 51–228

Krev interaction trapped protein 1

OrganismNot specified

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 227–255	Not recorded	Malcavernin × 2 （Q9BSQ5）	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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 227–255	Not recorded	Malcavernin × 2 （Q9BSQ5）	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

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 9PVG	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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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
4DXA Co-crystal structure of Rap1 in complex with KRIT1 Deposited 2012-02-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 420–736（317 aa） Fragment：FERM domain	Not recorded	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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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

14 other PDB entries and 23 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 E； PDBConstruct 1–29； UniProt 227–255 Author chain F； PDBConstruct 1–29； UniProt 227–255

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9pvg
Deposition date deposition_date	2025-08-01
最后修订 last_revision	2026-01-28
Structure title title	Co-crystal structure of two CCM2 PTB domains bound to a KRIT1 peptide encompassing NPxF2 and NPxF3
Keywords keywords	PTB domain, NPxY, NPxF, Cerebral Cavernous Malformations, CCM, protein-protein, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	31.96 Å
Radius of gyration Rg (electron density) rg_electron	31.42 Å
Forward intensity I(0) i0	65017700.00
Molecular weight molecular_weight	64895.0 kDa
Excluded volume excluded_volume	81904 Å³
Envelope volume envelope_volume	107800 Å³
Hydration-shell volume shell_volume	30403 Å³
Envelope diameter envelope_diameter	109.2 Å
Shell Rg shell_rg	35.92 Å
Envelope Rg envelope_rg	31.22 Å
Shape Rg shape_rg	31.42 Å
Total Rg total_rg	31.85 Å
Total atoms total_atoms	4573
Residues n_residues	584
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	108.8 Å
Rg (real space) rg_real	32.20 Å
Rg uncertainty (real space) rg_real_error	0.84 Å
I(0) (real space) i0_real	6.5020e+07
I(0) uncertainty (real space) i0_real_error	1.1130e+06
Rg (reciprocal space) rg_reciprocal	32.10 Å
I(0) (reciprocal space) i0_reciprocal	65010000.0000
Solution quality estimate total_estimate	0.6560
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	28.3 Å
Skewness Skewness skewness	0.468
Kurtosis Kurtosis kurtosis	-0.408
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	53330000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.776; Stabil: 1.000; Sysdev: 0.169; Positv: 1.000; Valcen: 0.843; Smooth: 0.847

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Malcavernin
Molecular weight formula_weight	19523.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4573

GSERVEPDRLLSDYIEKEVKYLGQLTSIPGYLNPSSRTEILHFIDNAKRAHQLPGHLTQEHDAVLSLSAYNVKLAWRDGEDIILRVPIHDIAAVSYVRDDAAHLVVLKTAQDPGISPSQSLCAESSRGLSAGSLSESAVGPVEACCLVILAAESKVAAEELCCLLGQVFQVVYTESTIDF

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	3352.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

TCIYNPLFGSDLQYTNRVDKVVINPYFGL

▶

8. Citations (1)

▶

Unit-cell length a length_a	45.198 Å
Unit-cell length b length_b	120.441 Å
Unit-cell length c length_c	67.778 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.73 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2497
R_work r_work	0.2470
R_free r_free	0.2967

fit	/app/data/saxs_computation/pv/9pvg/9pvg.fit
pddf	/app/data/pr_computation/pv/9pvg/9pvg.pr.out
profile	/app/data/saxs_computation/pv/9pvg/9pvg.dat

Co-crystal structure of two CCM2 PTB domains bound to a KRIT1 peptide encompassing NPxF2 and NPxF3

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

Malcavernin

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)