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5d68

Crystal structure of KRIT1 ARD-FERM

Method: X-RAY DIFFRACTION Dmax: 173.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 52–529 Fragment：ARD-FERM domain (UNP residues 52-529) No other associated polymer 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 52–529 Fragment：ARD-FERM domain (UNP residues 52-529) No other associated polymer 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 52–529 Fragment：ARD-FERM domain (UNP residues 52-529) No other associated polymer 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

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 5D68 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 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 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
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
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 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 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 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KRIT1_HUMAN
Isoform O00522-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 9–486； UniProt 52–529 Author chain B； PDBConstruct 9–486； UniProt 52–529 Author chain C； PDBConstruct 9–486； UniProt 52–529

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 5d68

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5d68
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5d68
Deposition date deposition_date2015-08-11
Structure title titleCrystal structure of KRIT1 ARD-FERM
Keywords keywordsAnkyrin Repeat Domain, FERM domain, Cerebral Cavernous Malformations, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier47.27 Å
Radius of gyration Rg (electron density) rg_electron47.09 Å
Forward intensity I(0) i0324290000.00
Molecular weight molecular_weight150330.0 kDa
Excluded volume excluded_volume189340 ų
Envelope volume envelope_volume281040 ų
Hydration-shell volume shell_volume52728 ų
Envelope diameter envelope_diameter168.5 Å
Shell Rg shell_rg47.73 Å
Envelope Rg envelope_rg46.12 Å
Shape Rg shape_rg47.10 Å
Total Rg total_rg47.06 Å
Total atoms total_atoms10586
Residues n_residues1301
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax173.1 Å
Rg (real space) rg_real47.65 Å
Rg uncertainty (real space) rg_real_error2.29 Å
I(0) (real space) i0_real3.2430e+08
I(0) uncertainty (real space) i0_real_error7.0050e+06
Rg (reciprocal space) rg_reciprocal47.27 Å
I(0) (reciprocal space) i0_reciprocal324100000.0000
Solution quality estimate total_estimate0.7844
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary52.5 Å
Skewness Skewness skewness0.464
Kurtosis Kurtosis kurtosis-0.293
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15550000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.773; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.872; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)