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- PDB-7s47: Integrin beta5(743-774)-linker-PAK4cat(D440N/S474E) -

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Basic information

Entry
Database: PDB / ID: 7s47
TitleIntegrin beta5(743-774)-linker-PAK4cat(D440N/S474E)
Components
  • Integrin beta-5
  • Integrin beta-5, Isoform 2 of Serine/threonine-protein kinase PAK 4 chimera
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) / integrin complex / wound healing, spreading of epidermal cells / Molecules associated with elastic fibres / cell adhesion mediated by integrin / Syndecan interactions / stress fiber assembly / endodermal cell differentiation ...integrin alphav-beta5 complex / epithelial cell-cell adhesion / Cross-presentation of particulate exogenous antigens (phagosomes) / integrin complex / wound healing, spreading of epidermal cells / Molecules associated with elastic fibres / cell adhesion mediated by integrin / Syndecan interactions / stress fiber assembly / endodermal cell differentiation / TGF-beta receptor signaling activates SMADs / Smooth Muscle Contraction / ECM proteoglycans / Integrin cell surface interactions / phagocytic vesicle / transforming growth factor beta receptor signaling pathway / cell-matrix adhesion / integrin-mediated signaling pathway / cell-cell adhesion / integrin binding / cell migration / virus receptor activity / receptor complex / non-specific serine/threonine protein kinase / focal adhesion / cell surface / extracellular exosome / metal ion binding / plasma membrane
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / 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.
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Isoform 2 of Serine/threonine-protein kinase PAK 4 / Integrin beta-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin beta-5, Isoform 2 of Serine/threonine-protein kinase PAK 4 chimera
B: Integrin beta-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4883
Polymers46,9822
Non-polymers5061
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-3 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.321, 62.321, 178.609
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 Integrin beta-5, Isoform 2 of Serine/threonine-protein kinase PAK 4 chimera / p21-activated kinase 4 / PAK-4


Mass: 43060.586 Da / Num. of mol.: 1 / Mutation: D440N,S474E
Source method: isolated from a genetically manipulated source
Details: Chimeric protein of Integrin beta 5 (743-744-SSGSSGSS GSSG-PAK4 kinase (109-426)
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB5, PAK4, KIAA1142 / Production host: Escherichia coli (E. coli)
References: UniProt: P18084, UniProt: O96013-2, non-specific serine/threonine protein kinase
#2: Protein/peptide Integrin beta-5


Mass: 3921.489 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Integrin beta 5 cytosolic domain ( 743- KLLVTIHDRREFAKFQSERSRARYEMASNPLY-774 )
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB5 / Production host: Escherichia coli (E. coli) / References: UniProt: P18084
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.85 Å3/Da / Density % sol: 33.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium acetate pH 4.0, 0.7 M diammonium phosphate

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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: ADSC QUANTUM 315 / Detector: CCD / 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: 2→50.01 Å / Num. obs: 24672 / % possible obs: 99.8 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.059 / Rrim(I) all: 0.176 / Χ2: 0.993 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.078.91.824070.6120.73710.896100
2.07-2.158.91.43724120.7440.50210.887100
2.15-2.258.91.04524120.8510.36510.991100
2.25-2.378.90.68124190.9390.2370.7220.936100
2.37-2.528.90.47824330.9650.1670.5070.952100
2.52-2.718.90.29824430.9840.1040.3161.035100
2.71-2.998.90.17324620.9910.0610.1841.052100
2.99-3.428.80.10624770.9950.0370.1131.093100
3.42-4.318.50.07125210.9970.0250.0761.06499.8
4.31-50.018.10.05626860.9970.0210.061.02598.4

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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: 2→50.01 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.125 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 1258 5.1 %RANDOM
Rwork0.1935 ---
obs0.1957 23367 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.63 Å2 / Biso mean: 36.138 Å2 / Biso min: 18.66 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 10 103 2463
Biso mean--56.26 39.72 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192415
X-RAY DIFFRACTIONr_bond_other_d0.0020.022402
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9863269
X-RAY DIFFRACTIONr_angle_other_deg1.01435519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.335296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95223.208106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37215438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5351522
X-RAY DIFFRACTIONr_chiral_restr0.1020.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212677
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02539
LS refinement shellResolution: 2.001→2.053 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 90 -
Rwork0.271 1656 -
all-1746 -
obs--97.92 %
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)
11.01220.0128-0.39790.5416-0.50231.69050.0214-0.1332-0.0321-0.0253-0.0587-0.0410.03120.09650.03730.0675-0.05870.04970.0761-0.03480.0402-21.248511.7722-6.6913
25.08127.2847-5.72711.288-6.005512.8220.63470.21560.61980.76620.31090.7178-0.8293-0.1449-0.94560.19790.02530.15230.17430.04350.2465-26.23223.0645-2.3291
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A300 - 314
2X-RAY DIFFRACTION1A315 - 328
3X-RAY DIFFRACTION1A329 - 352
4X-RAY DIFFRACTION1A353 - 361
5X-RAY DIFFRACTION1A362 - 375
6X-RAY DIFFRACTION1A376 - 381
7X-RAY DIFFRACTION1A382 - 401
8X-RAY DIFFRACTION1A402 - 411
9X-RAY DIFFRACTION1A412 - 462
10X-RAY DIFFRACTION1A463 - 475
11X-RAY DIFFRACTION1A476 - 511
12X-RAY DIFFRACTION1A512 - 534
13X-RAY DIFFRACTION1A535 - 573
14X-RAY DIFFRACTION1A574 - 589
15X-RAY DIFFRACTION2B763 - 768

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