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- PDB-4dx8: ICAP1 in complex with KRIT1 N-terminus -

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Basic information

Entry
Database: PDB / ID: 4dx8
TitleICAP1 in complex with KRIT1 N-terminus
Components
  • Integrin beta-1-binding protein 1
  • Krev interaction trapped protein 1
KeywordsPROTEIN BINDING / Protein-protein complex / PTB domain / Nudix fold / Protein-protein interaction / Membrane / nucleus
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 / myoblast migration / negative regulation of substrate adhesion-dependent cell spreading / GTPase regulator activity / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / endothelium development / 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 / myoblast migration / negative regulation of substrate adhesion-dependent cell spreading / GTPase regulator activity / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / endothelium development / negative regulation of focal adhesion assembly / integrin activation / negative regulation of cell migration involved in sprouting angiogenesis / tube formation / negative regulation of fibroblast migration / cellular response to fibroblast growth factor stimulus / regulation of establishment of cell polarity / GDP-dissociation inhibitor activity / negative regulation of endothelial cell migration / small GTPase-mediated signal transduction / regulation of GTPase activity / positive regulation of Notch signaling pathway / receptor clustering / negative regulation of endothelial cell proliferation / positive regulation of focal adhesion assembly / regulation of cell adhesion mediated by integrin / positive regulation of cell division / centriolar satellite / positive regulation of protein targeting to membrane / cellular response to vascular endothelial growth factor stimulus / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / positive regulation of stress fiber assembly / Notch signaling pathway / ruffle / phosphatidylinositol-4,5-bisphosphate binding / activation of protein kinase B activity / blood vessel diameter maintenance / positive regulation of endothelial cell migration / negative regulation of angiogenesis / cell-matrix adhesion / cell redox homeostasis / negative regulation of protein binding / protein localization to plasma membrane / integrin-mediated signaling pathway / cell periphery / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / cell-cell junction / cell migration / integrin binding / lamellipodium / microtubule binding / angiogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / cytoskeleton / nuclear body / 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
KRIT, N-terminal Nudix domain, NPxY motif-rich region / 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 ...KRIT, N-terminal Nudix domain, NPxY motif-rich region / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / 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: 2.54 Å
AuthorsLiu, W. / Draheim, K. / Zhang, R. / Calderwood, D.A. / Boggon, T.J.
CitationJournal: Mol.Cell / Year: 2013
Title: Mechanism for KRIT1 Release of ICAP1-Mediated Suppression of Integrin Activation.
Authors: Liu, W. / Draheim, K.M. / Zhang, R. / Calderwood, D.A. / Boggon, T.J.
History
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Mar 13, 2013Group: Database references
Revision 1.3Sep 2, 2020Group: Database references / Derived calculations / Structure summary
Category: struct_keywords / struct_ref_seq_dif / struct_site
Item: _struct_keywords.text / _struct_ref_seq_dif.details ..._struct_keywords.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin beta-1-binding protein 1
B: Integrin beta-1-binding protein 1
D: Integrin beta-1-binding protein 1
E: Integrin beta-1-binding protein 1
H: Krev interaction trapped protein 1
I: Krev interaction trapped protein 1
J: Krev interaction trapped protein 1
K: Krev interaction trapped protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,56124
Polymers159,2828
Non-polymers1,27816
Water25214
1
A: Integrin beta-1-binding protein 1
J: Krev interaction trapped protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0605
Polymers39,8212
Non-polymers2403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-10 kcal/mol
Surface area15240 Å2
MethodPISA
2
B: Integrin beta-1-binding protein 1
H: Krev interaction trapped protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3008
Polymers39,8212
Non-polymers4796
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-11 kcal/mol
Surface area15730 Å2
MethodPISA
3
D: Integrin beta-1-binding protein 1
I: Krev interaction trapped protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1406
Polymers39,8212
Non-polymers3204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-11 kcal/mol
Surface area13920 Å2
MethodPISA
4
E: Integrin beta-1-binding protein 1
K: Krev interaction trapped protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0605
Polymers39,8212
Non-polymers2403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-11 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.898, 157.977, 152.006
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D
41E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4 / Auth seq-ID: 58 - 196 / Label seq-ID: 12 - 150

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3DC
4ED

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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.: 4 / Fragment: PTB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ICAP1, Integrin cytoplasmic domain-associated protein 1 (ICAP1), ITGB1BP1
Plasmid: pET-32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14713
#2: Protein
Krev interaction trapped protein 1 / Krev interaction trapped 1 / Cerebral cavernous malformations 1 protein


Mass: 22911.543 Da / Num. of mol.: 4 / Fragment: Nudix domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CCM1, Krev interaction trapped protein 1 (KRIT1), KRIT1
Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00522
#3: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.9 Å3/Da / Density % sol: 57.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.06M AmSO4, 0.2M Ammonium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2011
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. all: 61242 / Num. obs: 61242 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 85.4 Å2 / Rsym value: 0.087 / Net I/σ(I): 19.4
Reflection shellResolution: 2.54→2.64 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 6068 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.942 / SU ML: 0.182 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.322 / ESU R Free: 0.244 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2517 3097 5.1 %RANDOM
Rwork0.22 ---
all0.2216 61048 --
obs0.2216 61048 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 283.36 Å2 / Biso mean: 102.7818 Å2 / Biso min: 52.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å20 Å2
2---1.09 Å20 Å2
3---2.34 Å2
Refinement stepCycle: LAST / Resolution: 2.54→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8098 0 16 14 8128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.028228
X-RAY DIFFRACTIONr_angle_refined_deg1.0021.98311109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7695982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74623.977352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.496151478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6641550
X-RAY DIFFRACTIONr_chiral_restr0.0650.21301
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215969
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1038 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.340.5
BMEDIUM POSITIONAL0.490.5
DMEDIUM POSITIONAL0.480.5
EMEDIUM POSITIONAL0.410.5
AMEDIUM THERMAL4.212
BMEDIUM THERMAL4.662
DMEDIUM THERMAL4.182
EMEDIUM THERMAL3.632
LS refinement shellResolution: 2.54→2.602 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 210 -
Rwork0.359 3804 -
all-4014 -
obs--93.11 %
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)
14.30110.763-0.8152.5181.1674.16180.05370.1567-0.21310.0406-0.01580.06830.3250.0385-0.03790.2291-0.0380.00740.2508-0.09390.051613.46642.39654.12
22.46910.31620.60414.1487-1.55194.572-0.07630.1194-0.02670.17130.0473-0.1770.00550.37810.02890.1457-0.0216-0.04630.3165-0.04770.028533.07559.50166.359
32.9573-0.1185-0.53163.2827-0.31543.7443-0.0458-0.04040.10330.04770.1854-0.23580.03270.032-0.13960.18190.07680.05680.2334-0.05010.066538.57321.88218.964
44.57870.57930.83332.29690.66684.94770.13930.10490.724-0.0802-0.12320.1835-0.22280.0226-0.01610.17950.07710.06640.1989-0.04330.179716.67438.92825.465
53.7652-0.3655-0.73466.36730.01593.7415-0.05760.35370.4295-0.4150.24980.989-0.0306-0.3509-0.19230.1788-0.1136-0.12410.38010.13690.236917.98583.75850.132
614.2529-2.46040.112411.9951-1.58215.3761-0.0591-1.3386-2.81030.6880.2252.30510.5631-0.417-0.16590.64530.07660.20770.69020.26710.959822.6082.45437.873
711.6901-2.76612.23754.416-0.22918.372-0.7772-0.82131.77240.4048-0.31540.9848-1.3617-0.94331.09270.894-0.0812-0.05540.5995-0.39220.8698-7.88858.54170.326
817.74653.68884.09835.61882.40866.85320.30570.4278-2.5562-0.6759-0.14571.51040.0517-0.8802-0.161.04030.3168-0.28591.013-0.05391.24572.64523.0715.198
91.5648-0.46012.1294.3476-0.56768.78910.00290.0037-0.03150.06830.19760.268-0.0982-0.3495-0.20050.1067-0.0562-0.00820.2568-0.04350.102421.04558.32264.002
104.8-0.9524-8.33877.1806-1.258716.1309-0.00920.3624-0.02680.0328-0.05680.1257-0.1399-0.98060.06610.11570.0743-0.02110.3312-0.02150.125326.30722.4218.591
1112.3156-1.3281-5.34513.2025.527116.56190.33410.35950.658-0.12010.1297-0.1782-0.569-0.1046-0.46380.2317-0.0760.01170.1556-0.00160.122116.48254.19955.985
127.5743-0.3343-1.13496.29357.130715.1337-0.06640.17150.1915-0.0463-0.1471-0.10290.53290.28080.21350.17450.0930.04150.16-0.02170.09220.20526.94625.113
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 196
2X-RAY DIFFRACTION2B58 - 196
3X-RAY DIFFRACTION3D58 - 196
4X-RAY DIFFRACTION4E58 - 196
5X-RAY DIFFRACTION5H8 - 179
6X-RAY DIFFRACTION6I12 - 179
7X-RAY DIFFRACTION7J8 - 179
8X-RAY DIFFRACTION8K13 - 179
9X-RAY DIFFRACTION9H180 - 197
10X-RAY DIFFRACTION10I180 - 197
11X-RAY DIFFRACTION11J180 - 197
12X-RAY DIFFRACTION12K180 - 197

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