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- PDB-5d68: Crystal structure of KRIT1 ARD-FERM -

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Basic information

Entry
Database: PDB / ID: 5d68
TitleCrystal structure of KRIT1 ARD-FERM
ComponentsKrev interaction trapped protein 1
KeywordsSIGNALING PROTEIN / Ankyrin Repeat Domain / FERM domain / Cerebral Cavernous Malformations
Function / homology
Function and homology information


GTPase regulator activity / endothelium development / integrin activation / negative regulation of endothelial cell migration / regulation of establishment of cell polarity / small GTPase-mediated signal transduction / negative regulation of endothelial cell proliferation / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / phosphatidylinositol-4,5-bisphosphate binding ...GTPase regulator activity / endothelium development / integrin activation / negative regulation of endothelial cell migration / regulation of establishment of cell polarity / small GTPase-mediated signal transduction / negative regulation of endothelial cell proliferation / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / phosphatidylinositol-4,5-bisphosphate binding / negative regulation of angiogenesis / cell redox homeostasis / cell-cell junction / microtubule binding / angiogenesis / cytoskeleton / protein-containing complex / extracellular space / plasma membrane / cytoplasm
Similarity search - Function
KRIT, N-terminal NPxY motif-rich region / Krev interaction trapped protein 1, FERM domain C-lobe / KRIT, N-terminal NPxY motif-rich domain superfamily / NUDIX, or N-terminal NPxY motif-rich, region of KRIT / Ankyrin repeats (many copies) / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain ...KRIT, N-terminal NPxY motif-rich region / Krev interaction trapped protein 1, FERM domain C-lobe / KRIT, N-terminal NPxY motif-rich domain superfamily / NUDIX, or N-terminal NPxY motif-rich, region of KRIT / Ankyrin repeats (many copies) / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Krev interaction trapped protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.908 Å
AuthorsZhang, R. / Li, X. / Boggon, T.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS085078 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103403 United States
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural analysis of the KRIT1 ankyrin repeat and FERM domains reveals a conformationally stable ARD-FERM interface.
Authors: Zhang, R. / Li, X. / Boggon, T.J.
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Krev interaction trapped protein 1
B: Krev interaction trapped protein 1
C: Krev interaction trapped protein 1


Theoretical massNumber of molelcules
Total (without water)168,4633
Polymers168,4633
Non-polymers00
Water1,18966
1
A: Krev interaction trapped protein 1


Theoretical massNumber of molelcules
Total (without water)56,1541
Polymers56,1541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Krev interaction trapped protein 1


Theoretical massNumber of molelcules
Total (without water)56,1541
Polymers56,1541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Krev interaction trapped protein 1


Theoretical massNumber of molelcules
Total (without water)56,1541
Polymers56,1541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.734, 80.242, 213.145
Angle α, β, γ (deg.)90.00, 91.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Krev interaction trapped protein 1 / Krev interaction trapped 1 / Cerebral cavernous malformations 1 protein


Mass: 56154.168 Da / Num. of mol.: 3 / Fragment: ARD-FERM domain (UNP residues 52-529)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRIT1, CCM1 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / References: UniProt: O00522
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.05 M HEPES, pH 7.3, 8% ethylene glycol, 8% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 19, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 46892 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.192 / Net I/σ(I): 7.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.899 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1760refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 4DXA & 4HB5

4dxa

4hb5


Resolution: 2.908→49.369 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 2376 5.07 %5.07
Rwork0.2066 ---
obs0.2086 46862 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.908→49.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10586 0 0 66 10652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410827
X-RAY DIFFRACTIONf_angle_d0.78814642
X-RAY DIFFRACTIONf_dihedral_angle_d14.2254080
X-RAY DIFFRACTIONf_chiral_restr0.0351611
X-RAY DIFFRACTIONf_plane_restr0.0041870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9077-2.96710.29851270.29872517X-RAY DIFFRACTION95
2.9671-3.03160.32391240.29222583X-RAY DIFFRACTION100
3.0316-3.10210.3581180.28322678X-RAY DIFFRACTION100
3.1021-3.17970.34461610.29342533X-RAY DIFFRACTION100
3.1797-3.26560.31411410.2732607X-RAY DIFFRACTION100
3.2656-3.36170.26511310.25932613X-RAY DIFFRACTION100
3.3617-3.47020.32151360.24742607X-RAY DIFFRACTION100
3.4702-3.59420.2881520.23882608X-RAY DIFFRACTION100
3.5942-3.7380.25431400.23142646X-RAY DIFFRACTION100
3.738-3.90810.26621470.2122592X-RAY DIFFRACTION100
3.9081-4.1140.2441490.1982609X-RAY DIFFRACTION100
4.114-4.37160.21591420.16582628X-RAY DIFFRACTION100
4.3716-4.70890.18481340.14562629X-RAY DIFFRACTION100
4.7089-5.18240.20921470.15042605X-RAY DIFFRACTION100
5.1824-5.93120.20851440.17012640X-RAY DIFFRACTION100
5.9312-7.46850.21121430.1812688X-RAY DIFFRACTION100
7.4685-49.37610.17521400.16322703X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2417-0.02750.07732.15931.35676.1756-0.2953-0.1726-0.01240.02320.245-0.175-0.2410.477-0.03420.2678-0.0664-0.01960.30640.04460.3629126.0699-16.4298-22.13
23.88960.7786-1.13873.33690.35924.606-0.32750.5411-0.3658-0.10510.01270.22890.852-0.6230.3390.4403-0.16820.08330.3385-0.05750.3363114.1401-28.6149-26.3664
33.25240.283-0.67111.89331.04373.0551-0.4124-0.0935-0.57080.51780.33530.07621.1826-0.19320.60470.6778-0.01950.14150.30870.02280.4627106.3121-32.8934-5.5655
43.72491.373-1.69183.7340.6514.3933-0.20370.1351-0.0958-0.0816-0.16970.48860.4833-1.06710.280.3727-0.088-0.00190.3666-0.03830.36498.8254-24.2321-1.0725
52.80610.281-0.49552.66570.08874.4014-0.02210.20040.0946-0.40460.0425-0.4911-0.42430.76710.04580.3482-0.0960.04560.37880.00730.3413115.0784-15.80430.0776
60.46020.1658-1.28780.4576-0.44083.5211-0.32050.2538-0.1426-0.0234-0.18670.19030.607-0.8120.16240.3388-0.16440.05270.395-0.080.469894.5033-25.289710.3881
73.19481.0541-0.98821.71090.85653.6093-0.2645-0.2405-0.39510.2748-0.002-0.43270.8550.3710.35170.63230.00680.08120.2970.01580.4321100.5273-29.692730.1289
81.2550.3468-0.07363.1127-0.87775.3373-0.27340.2515-0.46340.50980.23910.69281.6842-1.2990.15540.6993-0.2080.20040.521-0.06720.501889.9881-31.962425.7943
92.0132.0893-1.09466.9367-1.35762.38850.7039-0.69940.04791.1039-0.7624-0.4615-0.434-0.07070.18220.4031-0.0031-0.02070.3907-0.00290.3769103.8056-7.637116.1512
102.59240.4472-0.99235.345-1.47316.14670.21640.25710.62140.4125-0.27350.2719-1.0998-0.1316-0.00370.50390.04140.01770.31630.05440.389298.9168-3.333113.5948
113.11970.55710.48055.94060.01656.33140.2762-0.14130.30610.1606-0.38940.4899-0.8856-1.0768-0.10830.52760.1064-0.01270.44330.09940.480696.5534-2.51039.009
122.91310.4263-1.93084.2451-0.25097.73690.3802-0.53750.21660.2708-0.1945-0.6323-0.39430.8493-0.1540.3532-0.1498-0.04790.37580.00210.3891154.150610.849193.7744
130.96040.99480.47133.322.12433.82360.1669-0.47860.06670.4566-0.71330.54930.2468-0.94850.40920.3311-0.10080.06960.6466-0.06520.4045134.89311.1986.2952
142.33520.1647-1.20310.8501-0.33684.22770.1612-0.1295-0.18170.0674-0.2192-0.0553-0.2012-0.0370.04460.2396-0.0703-0.03270.23580.00010.3225137.9433-7.470264.9732
155.93292.2061-0.95582.35510.55482.04180.1910.40040.7474-0.6102-0.22380.3352-0.7273-0.4673-0.01220.42660.2323-0.10220.4492-0.03710.41129.7363-6.461241.0357
161.7975-0.08181.13052.36470.06265.41580.2542-0.1075-0.3917-0.108-0.20680.33790.1719-0.8821-0.05120.28420.0305-0.02680.3569-0.06310.3433129.6282-14.704848.7047
174.34580.21251.4893.11430.06844.20420.17770.2029-0.44990.022-0.557-0.8320.38821.04770.17250.31510.051-0.08560.46970.1420.5613153.3134-17.172757.3364
183.43243.1092-2.04386.8829-1.224.70980.004-0.1028-0.2958-0.021-0.4457-0.57451.05230.51820.29720.37620.1183-0.1040.4610.12580.5033150.4656-24.320264.8291
192.8246-0.51921.01314.0895-0.92336.2766-0.09920.0688-0.0415-0.2898-0.10530.0488-0.1351-0.40070.17890.3479-0.00440.00460.2967-0.04990.284287.3558-21.519747.0409
201.9827-0.71150.98961.9071.36964.7289-0.11060.24750.2127-0.3315-0.15650.3007-0.7769-0.20340.35680.43310.0354-0.04770.30150.03120.405987.2323-3.354363.6919
210.8429-0.6653-0.59442.60730.23955.1781-0.052-0.0151-0.01350.0241-0.14120.0479-0.39830.09980.13490.229-0.0542-0.04690.21910.01420.337794.7653-5.196676.9138
223.0751-0.1939-0.5587.41931.50186.7764-0.2661-0.29510.22640.31040.24170.4387-0.6647-1.0042-0.03970.45390.1189-0.06560.4717-0.06970.335688.68365.673198.577
231.8399-0.7678-1.11992.09830.03266.1184-0.4574-0.5092-0.25750.15680.4734-0.07120.7940.12650.1110.29470.0057-0.02870.40540.03970.506105.9334-11.110387.2033
244.2272-0.2978-1.0714.28481.67546.4839-0.2591-0.284-0.09090.35960.0699-0.57240.2211.02930.20470.2596-0.012-0.01370.4863-0.00830.4889112.5068-9.540384.9613
253.7606-0.6807-0.12377.8007-1.59234.2505-0.203-0.56690.37460.62730.2181-0.7119-0.23991.00950.03010.3041-0.02540.05810.6423-0.07790.5058114.2651-8.763380.6422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 288 through 342 )
2X-RAY DIFFRACTION2chain 'A' and (resid 343 through 414 )
3X-RAY DIFFRACTION3chain 'A' and (resid 415 through 443 )
4X-RAY DIFFRACTION4chain 'A' and (resid 444 through 479 )
5X-RAY DIFFRACTION5chain 'A' and (resid 480 through 504 )
6X-RAY DIFFRACTION6chain 'A' and (resid 505 through 541 )
7X-RAY DIFFRACTION7chain 'A' and (resid 542 through 597 )
8X-RAY DIFFRACTION8chain 'A' and (resid 598 through 630 )
9X-RAY DIFFRACTION9chain 'A' and (resid 631 through 662 )
10X-RAY DIFFRACTION10chain 'A' and (resid 663 through 701 )
11X-RAY DIFFRACTION11chain 'A' and (resid 702 through 730 )
12X-RAY DIFFRACTION12chain 'B' and (resid 288 through 333 )
13X-RAY DIFFRACTION13chain 'B' and (resid 334 through 479 )
14X-RAY DIFFRACTION14chain 'B' and (resid 480 through 541 )
15X-RAY DIFFRACTION15chain 'B' and (resid 542 through 597 )
16X-RAY DIFFRACTION16chain 'B' and (resid 598 through 644 )
17X-RAY DIFFRACTION17chain 'B' and (resid 645 through 701 )
18X-RAY DIFFRACTION18chain 'B' and (resid 702 through 736 )
19X-RAY DIFFRACTION19chain 'C' and (resid 288 through 403 )
20X-RAY DIFFRACTION20chain 'C' and (resid 404 through 479 )
21X-RAY DIFFRACTION21chain 'C' and (resid 480 through 541 )
22X-RAY DIFFRACTION22chain 'C' and (resid 542 through 630 )
23X-RAY DIFFRACTION23chain 'C' and (resid 631 through 662 )
24X-RAY DIFFRACTION24chain 'C' and (resid 663 through 701 )
25X-RAY DIFFRACTION25chain 'C' and (resid 702 through 729 )

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