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- PDB-4jif: Co-crystal structure of ICAP1 PTB domain in complex with a KRIT1 ... -

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Basic information

Entry
Database: PDB / ID: 4jif
TitleCo-crystal structure of ICAP1 PTB domain in complex with a KRIT1 peptide
Components
  • Integrin beta-1-binding protein 1
  • Krev interaction trapped protein 1
KeywordsSIGNALING PROTEIN / PTB fold / Integrin signaling / Integrin binding
Function / homology
Function and homology information


negative regulation of protein targeting to membrane / regulation of integrin-mediated signaling pathway / negative regulation of cell adhesion involved in substrate-bound cell migration / biomineral tissue development / negative regulation of substrate adhesion-dependent cell spreading / myoblast migration / GTPase regulator activity / endothelium development / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of focal adhesion assembly ...negative regulation of protein targeting to membrane / regulation of integrin-mediated signaling pathway / negative regulation of cell adhesion involved in substrate-bound cell migration / biomineral tissue development / negative regulation of substrate adhesion-dependent cell spreading / myoblast migration / GTPase regulator activity / endothelium development / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of focal adhesion assembly / tube formation / integrin activation / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of fibroblast migration / cellular response to fibroblast growth factor stimulus / negative regulation of endothelial cell migration / regulation of establishment of cell polarity / GDP-dissociation inhibitor activity / small GTPase-mediated signal transduction / regulation of GTPase activity / receptor clustering / negative regulation of endothelial cell proliferation / positive regulation of Notch signaling pathway / positive regulation of focal adhesion assembly / regulation of cell adhesion mediated by integrin / positive regulation of cell division / positive regulation of protein targeting to membrane / centriolar satellite / cellular response to vascular endothelial growth factor stimulus / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / Notch signaling pathway / positive regulation of stress fiber assembly / ruffle / phosphatidylinositol-4,5-bisphosphate binding / blood vessel diameter maintenance / activation of protein kinase B activity / negative regulation of angiogenesis / cell-matrix adhesion / cell redox homeostasis / positive regulation of endothelial cell migration / negative regulation of protein binding / cell periphery / integrin-mediated signaling pathway / protein localization to plasma membrane / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / cell-cell junction / cell migration / integrin binding / lamellipodium / microtubule binding / angiogenesis / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / nuclear body / cytoskeleton / intracellular signal transduction / negative regulation of cell population proliferation / positive regulation of cell population proliferation / protein kinase binding / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Integrin binding protein, ICAP-1 / Beta-1 integrin binding protein / 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) / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / FERM central domain ...Integrin binding protein, ICAP-1 / Beta-1 integrin binding protein / 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) / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Krev interaction trapped protein 1 / Integrin beta-1-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsLiu, W. / Boggon, T.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Cocrystal structure of the ICAP1 PTB domain in complex with a KRIT1 peptide.
Authors: Liu, W. / Boggon, T.J.
History
DepositionMar 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrin beta-1-binding protein 1
B: Krev interaction trapped protein 1


Theoretical massNumber of molelcules
Total (without water)20,6352
Polymers20,6352
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-8 kcal/mol
Surface area7980 Å2
MethodPISA
2
A: Integrin beta-1-binding protein 1
B: Krev interaction trapped protein 1

A: Integrin beta-1-binding protein 1
B: Krev interaction trapped protein 1


Theoretical massNumber of molelcules
Total (without water)41,2714
Polymers41,2714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area5860 Å2
ΔGint-24 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.017, 81.017, 89.583
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Integrin beta-1-binding protein 1 / Integrin cytoplasmic domain-associated protein 1 / ICAP-1


Mass: 16909.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB1BP1, ICAP1 / Plasmid: PET32-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14713
#2: Protein/peptide Krev interaction trapped protein 1 / Krev interaction trapped 1 / Cerebral cavernous malformations 1 protein


Mass: 3726.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRIT1, CCM1 / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00522
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 18-20%PEG3350, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2012
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. all: 19620 / Num. obs: 19541 / Redundancy: 12.4 % / Biso Wilson estimate: 28.3 Å2 / Rsym value: 0.061
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 12.3 % / Num. unique all: 1927 / Rsym value: 0 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DX8

4dx8


Resolution: 1.701→32.666 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1001 5.11 %random
Rwork0.1956 ---
all0.1971 19666 --
obs0.1971 -99.53 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.872 Å2 / ksol: 0.339 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.8918 Å20 Å20 Å2
2---6.8918 Å2-0 Å2
3---13.7836 Å2
Refinement stepCycle: LAST / Resolution: 1.701→32.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 0 111 1286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071246
X-RAY DIFFRACTIONf_angle_d1.071698
X-RAY DIFFRACTIONf_dihedral_angle_d14.858479
X-RAY DIFFRACTIONf_chiral_restr0.077196
X-RAY DIFFRACTIONf_plane_restr0.005215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7005-1.79020.35811260.38382610X-RAY DIFFRACTION100
1.7902-1.90230.35991300.29732608X-RAY DIFFRACTION100
1.9023-2.04920.25561780.23552573X-RAY DIFFRACTION100
2.0492-2.25540.23591520.20862596X-RAY DIFFRACTION99
2.2554-2.58160.24561350.19022645X-RAY DIFFRACTION100
2.5816-3.25210.21561550.18852682X-RAY DIFFRACTION100
3.2521-32.67190.19251250.16962859X-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)
11.9068-0.40960.99383.88890.92393.6026-0.1284-0.3190.49690.21660.2957-0.5234-0.218-0.0586-0.08140.3060.0428-0.10650.2544-0.07670.274414.671223.99084.1154
23.0956-0.1319-0.71931.10360.42232.51880.0011-0.01390.075-0.09270.06660.15240.0317-0.1651-0.09920.24630.021-0.07960.1833-0.0380.28178.404220.2113.1223
32.1166-1.68745.55048.36721.51886.61160.181.10570.9043-1.3576-0.0301-1.2885-1.26932.27990.50280.4728-0.17330.09210.5274-0.11520.462424.901826.0556-5.2901
43.20551.29420.9645.9171.60322.03820.2048-0.2161-0.26810.0708-0.137-0.40180.13980.0623-0.06420.2018-0.0009-0.0320.18020.03040.189418.285520.60586.7799
54.4982-0.01650.75444.9661-0.6917.1128-0.201-0.198-0.67150.4728-0.00641.1977-0.0418-0.76270.30360.2797-0.01710.0440.3320.01170.53943.3479.46310.4726
60.86350.8579-0.39475.1972-0.70720.41250.1677-0.3427-0.11170.8389-0.4369-0.6131-0.15880.07190.16410.3329-0.0574-0.17010.27340.0450.282119.790818.631615.3336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 60:84)
2X-RAY DIFFRACTION2chain 'A' and (resseq 85:115)
3X-RAY DIFFRACTION3chain 'A' and (resseq 116:128)
4X-RAY DIFFRACTION4chain 'A' and (resseq 129:194)
5X-RAY DIFFRACTION5chain 'B' and (resseq 178:185)
6X-RAY DIFFRACTION6chain 'B' and (resseq 186:196)

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