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- PDB-7s48: PAK4cat in complex with Integrin beta5 760-770 peptide -

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Basic information

Entry
Database: PDB / ID: 7s48
TitlePAK4cat in complex with Integrin beta5 760-770 peptide
Components
  • Integrin beta-5
  • Serine/threonine-protein kinase PAK 4
KeywordsTRANSFERASE / serine/threonine kinase
Function / homology
Function and homology information


integrin alphav-beta5 complex / epithelial cell-cell adhesion / Cross-presentation of particulate exogenous antigens (phagosomes) / dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / wound healing, spreading of epidermal cells / integrin complex / Molecules associated with elastic fibres / RHOV GTPase cycle ...integrin alphav-beta5 complex / epithelial cell-cell adhesion / Cross-presentation of particulate exogenous antigens (phagosomes) / dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / wound healing, spreading of epidermal cells / integrin complex / Molecules associated with elastic fibres / RHOV GTPase cycle / cell adhesion mediated by integrin / Syndecan interactions / stress fiber assembly / RHOJ GTPase cycle / RHOQ GTPase cycle / endodermal cell differentiation / TGF-beta receptor signaling activates SMADs / RHOU GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / Smooth Muscle Contraction / RAC2 GTPase cycle / RAC3 GTPase cycle / ECM proteoglycans / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / phagocytic vesicle / RAC1 GTPase cycle / cytoskeleton organization / transforming growth factor beta receptor signaling pathway / cellular response to starvation / cell-matrix adhesion / integrin-mediated signaling pathway / adherens junction / regulation of cell growth / cell-cell adhesion / integrin binding / positive regulation of angiogenesis / cell migration / virus receptor activity / non-specific serine/threonine protein kinase / receptor complex / protein kinase activity / intracellular signal transduction / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / cell surface / Golgi apparatus / signal transduction / extracellular exosome / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain ...p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase PAK 4 / Integrin beta-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHa, B.H. / Boggon, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM138411 United States
CitationJournal: Commun Biol / Year: 2022
Title: Molecular basis for integrin adhesion receptor binding to p21-activated kinase 4 (PAK4)
Authors: Ha, B.H. / Yigit, S. / Natarajan, N. / Morse, E.M. / Calderwood, D.A. / Boggon, T.J.
History
DepositionSep 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PAK 4
B: Integrin beta-5


Theoretical massNumber of molelcules
Total (without water)40,4822
Polymers40,4822
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-3 kcal/mol
Surface area13620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.735, 61.735, 179.987
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Serine/threonine-protein kinase PAK 4 / p21-activated kinase 4 / PAK-4


Mass: 39123.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PAK4 catalytic domain (109-426) / Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Production host: Escherichia coli (E. coli)
References: UniProt: O96013, non-specific serine/threonine protein kinase
#2: Protein/peptide Integrin beta-5


Mass: 1358.505 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide of Integrin beta 5 cytosolic domain (760-Glu-Arg-Ser-Arg-Ala-Arg-Tyr-Glu-Met-Ala-Ser-770)
Source: (synth.) Homo sapiens (human) / References: UniProt: P18084
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl (pH 8.5) and 0.5 M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→50.01 Å / Num. obs: 28270 / % possible obs: 99.4 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.022 / Rrim(I) all: 0.078 / Χ2: 0.78 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9712.51.00127540.7750.28810.53799.7
1.97-2.0512.40.69727720.880.2020.7260.52699.7
2.05-2.1411.70.47927920.9460.1440.5010.58599.9
2.14-2.2510.60.35627620.9570.1140.3750.65199.8
2.25-2.3910.80.23427750.9770.0730.2450.67499
2.39-2.5812.70.16528290.9920.0470.1720.681100
2.58-2.8411.90.11528120.9950.0340.120.95299.9
2.84-3.2510.50.0828410.9970.0260.0851.07899
3.25-4.0911.80.05428680.9990.0160.0571.13399
4.09-50.01110.0430650.9990.0120.0421.00598.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0151refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FIF

4fif


Resolution: 1.9→50.01 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.408 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1475 5.2 %RANDOM
Rwork0.1795 ---
obs0.1816 26735 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.31 Å2 / Biso mean: 40.958 Å2 / Biso min: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2---1.02 Å20 Å2
3---2.04 Å2
Refinement stepCycle: final / Resolution: 1.9→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 0 119 2476
Biso mean---43.84 -
Num. residues----297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192423
X-RAY DIFFRACTIONr_bond_other_d0.0020.022410
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.9853283
X-RAY DIFFRACTIONr_angle_other_deg0.98935542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4395299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85823.143105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85715439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0331522
X-RAY DIFFRACTIONr_chiral_restr0.0960.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212687
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02535
LS refinement shellResolution: 1.902→1.951 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 110 -
Rwork0.279 1935 -
all-2045 -
obs--99.61 %
Refinement TLS params.Method: refined / Origin x: -20.9617 Å / Origin y: 11.63 Å / Origin z: -6.9231 Å
111213212223313233
T0.032 Å2-0.0215 Å20.0281 Å2-0.0534 Å2-0.0172 Å2--0.0353 Å2
L1.3109 °20.095 °2-0.0504 °2-0.6841 °2-0.4408 °2--1.0006 °2
S0.0699 Å °-0.1577 Å °-0.0159 Å °0.0687 Å °-0.021 Å °0.0745 Å °0.0111 Å °0.0346 Å °-0.0489 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A300 - 355
2X-RAY DIFFRACTION1A356 - 369
3X-RAY DIFFRACTION1A370 - 381
4X-RAY DIFFRACTION1A382 - 452
5X-RAY DIFFRACTION1A453 - 471
6X-RAY DIFFRACTION1A472 - 533
7X-RAY DIFFRACTION1A534 - 567
8X-RAY DIFFRACTION1A568 - 589

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