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- PDB-6jjx: Crystal Structure of KIBRA and Angiomotin complex -

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Basic information

Entry
Database: PDB / ID: 6jjx
TitleCrystal Structure of KIBRA and Angiomotin complex
Components
  • Peptide from Angiomotin
  • Protein KIBRA
KeywordsSIGNALING PROTEIN / WW tandem / PY tandem / KIBRA / Angiomotin / AMOT
Function / homology
Function and homology information


establishment of cell polarity involved in ameboidal cell migration / Signaling by Hippo / cell migration involved in gastrulation / blood vessel endothelial cell migration / Regulation of CDH11 function / positive regulation of embryonic development / negative regulation of organ growth / angiostatin binding / regulation of modification of postsynaptic actin cytoskeleton / hippo signaling ...establishment of cell polarity involved in ameboidal cell migration / Signaling by Hippo / cell migration involved in gastrulation / blood vessel endothelial cell migration / Regulation of CDH11 function / positive regulation of embryonic development / negative regulation of organ growth / angiostatin binding / regulation of modification of postsynaptic actin cytoskeleton / hippo signaling / gastrulation with mouth forming second / negative regulation of vascular permeability / cell-cell junction assembly / Signaling by Hippo / regulation of small GTPase mediated signal transduction / endocytic vesicle / positive regulation of cell size / positive regulation of blood vessel endothelial cell migration / bicellular tight junction / negative regulation of hippo signaling / vasculogenesis / stress fiber / positive regulation of stress fiber assembly / ruffle / signaling adaptor activity / regulation of cell migration / negative regulation of angiogenesis / actin filament / kinase binding / ruffle membrane / chemotaxis / intracellular protein localization / cell migration / signaling receptor activity / lamellipodium / actin cytoskeleton organization / cytoplasmic vesicle / angiogenesis / in utero embryonic development / transcription coactivator activity / positive regulation of MAPK cascade / postsynaptic density / negative regulation of cell population proliferation / external side of plasma membrane / perinuclear region of cytoplasm / glutamatergic synapse / cell surface / negative regulation of transcription by RNA polymerase II / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
WWC, C2 domain / : / Angiomotin / Angiomotin, C-terminal / : / Angiomotin C terminal / C2 domain / WW domain / C2 domain / C2 domain profile. ...WWC, C2 domain / : / Angiomotin / Angiomotin, C-terminal / : / Angiomotin C terminal / C2 domain / WW domain / C2 domain / C2 domain profile. / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily
Similarity search - Domain/homology
Angiomotin / Protein KIBRA
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLin, Z. / Yang, Z. / Ji, Z. / Zhang, M.
CitationJournal: Elife / Year: 2019
Title: Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity.
Authors: Lin, Z. / Yang, Z. / Xie, R. / Ji, Z. / Guan, K. / Zhang, M.
History
DepositionFeb 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein KIBRA
B: Protein KIBRA
D: Peptide from Angiomotin
C: Peptide from Angiomotin


Theoretical massNumber of molelcules
Total (without water)37,6494
Polymers37,6494
Non-polymers00
Water4,738263
1
A: Protein KIBRA
C: Peptide from Angiomotin


Theoretical massNumber of molelcules
Total (without water)18,8252
Polymers18,8252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein KIBRA
D: Peptide from Angiomotin


Theoretical massNumber of molelcules
Total (without water)18,8252
Polymers18,8252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.627, 72.283, 79.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-300-

HOH

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Components

#1: Protein Protein KIBRA / Kidney and brain protein / KIBRA / WW domain-containing protein 1


Mass: 16036.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Wwc1, Kiaa0869
Production host: Escherichia coli str. 'clone D i2' (bacteria)
References: UniProt: Q5SXA9
#2: Protein/peptide Peptide from Angiomotin


Mass: 2788.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMOT, KIAA1071 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4VCS5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 25% w/v pentaerythritol propoxylat 629 (17/8 PO/OH), 50mM MgCl2, 100mM Tris (pH 8.5)
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 26165 / % possible obs: 99.8 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 22.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1282 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J68

6j68


Resolution: 2→39.687 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.12
RfactorNum. reflection% reflection
Rfree0.2345 1286 4.93 %
Rwork0.2083 --
obs0.2096 26101 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→39.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 0 263 2517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082321
X-RAY DIFFRACTIONf_angle_d1.1423160
X-RAY DIFFRACTIONf_dihedral_angle_d14.634849
X-RAY DIFFRACTIONf_chiral_restr0.056325
X-RAY DIFFRACTIONf_plane_restr0.006417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9968-2.07670.32461470.25862598X-RAY DIFFRACTION96
2.0767-2.17120.2861410.24162728X-RAY DIFFRACTION100
2.1712-2.28570.29621370.23452757X-RAY DIFFRACTION100
2.2857-2.42890.24391250.2332748X-RAY DIFFRACTION100
2.4289-2.61640.29691550.23662726X-RAY DIFFRACTION100
2.6164-2.87960.27771260.23092771X-RAY DIFFRACTION100
2.8796-3.29610.26181490.2162790X-RAY DIFFRACTION100
3.2961-4.15210.20581480.17682806X-RAY DIFFRACTION100
4.1521-39.69480.18241580.19272891X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 65.3741 Å / Origin y: 27.5841 Å / Origin z: 99.9216 Å
111213212223313233
T0.2718 Å2-0.0007 Å2-0.0021 Å2-0.2471 Å2-0.0044 Å2--0.2753 Å2
L0.2755 °20.0553 °20.1058 °2-0.013 °20.0207 °2--0.0406 °2
S0.0208 Å °0.066 Å °-0.017 Å °-0.0214 Å °0.0156 Å °0.0039 Å °0.0206 Å °0.0419 Å °-0.0381 Å °
Refinement TLS groupSelection details: all

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