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- PDB-4xh2: Crystal structure of human paxillin LD4 motif in complex with Fab... -

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Basic information

Entry
Database: PDB / ID: 4xh2
TitleCrystal structure of human paxillin LD4 motif in complex with Fab fragment
Components
  • Fab Heavy ChainFragment antigen-binding
  • Fab Light ChainFragment antigen-binding
  • paxillin LD4
KeywordsCELL ADHESION / synthetic antibody / paxillin / LD motif / immunoglobulin / Fab fragment / complex / focal adhesion
Function / homology
Function and homology information


Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / vinculin binding / neuropilin binding / signal complex assembly / microtubule associated complex / growth hormone receptor signaling pathway / Smooth Muscle Contraction / endothelial cell migration / GAB1 signalosome ...Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / vinculin binding / neuropilin binding / signal complex assembly / microtubule associated complex / growth hormone receptor signaling pathway / Smooth Muscle Contraction / endothelial cell migration / GAB1 signalosome / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of stress fiber assembly / stress fiber / cell-matrix adhesion / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / cellular response to reactive oxygen species / transcription coregulator activity / cell cortex / beta-catenin binding / VEGFA-VEGFR2 Pathway / cell-cell junction / lamellipodium / protein phosphatase binding / cell adhesion / focal adhesion / signal transduction / plasma membrane / metal ion binding / cytosol
Similarity search - Function
Paxillin / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETYL GROUP / ACETATE ION / PHOSPHATE ION / Paxillin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNocula-Lugowska, M. / Lugowski, M. / Salgia, R. / Kossiakoff, A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Engineering Synthetic Antibody Inhibitors Specific for LD2 or LD4 Motifs of Paxillin.
Authors: Nocula-Lugowska, M. / Lugowski, M. / Salgia, R. / Kossiakoff, A.A.
History
DepositionJan 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2May 31, 2017Group: Other
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab Heavy Chain
B: Fab Light Chain
C: Fab Heavy Chain
D: Fab Light Chain
E: Fab Heavy Chain
F: Fab Light Chain
G: Fab Heavy Chain
H: Fab Heavy Chain
I: Fab Light Chain
J: Fab Heavy Chain
K: Fab Light Chain
L: Fab Light Chain
a: paxillin LD4
c: paxillin LD4
e: paxillin LD4
g: paxillin LD4
h: paxillin LD4
j: paxillin LD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,90144
Polymers299,49318
Non-polymers2,40826
Water28,0311556
1
A: Fab Heavy Chain
B: Fab Light Chain
a: paxillin LD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1005
Polymers49,9153
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Fab Heavy Chain
D: Fab Light Chain
c: paxillin LD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2877
Polymers49,9153
Non-polymers3714
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Fab Heavy Chain
F: Fab Light Chain
e: paxillin LD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,66710
Polymers49,9153
Non-polymers7527
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Fab Heavy Chain
I: Fab Light Chain
g: paxillin LD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2847
Polymers49,9153
Non-polymers3684
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
H: Fab Heavy Chain
L: Fab Light Chain
h: paxillin LD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3288
Polymers49,9153
Non-polymers4125
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
J: Fab Heavy Chain
K: Fab Light Chain
j: paxillin LD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2367
Polymers49,9153
Non-polymers3204
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)117.580, 138.120, 223.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 1 types, 6 molecules aceghj

#3: Protein/peptide
paxillin LD4


Mass: 1939.088 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P49023*PLUS

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Antibody , 2 types, 12 molecules ACEGHJBDFIKL

#1: Antibody
Fab Heavy Chain / Fragment antigen-binding


Mass: 24261.975 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Details (production host): phoA promoter / Production host: Escherichia coli (E. coli)
#2: Antibody
Fab Light Chain / Fragment antigen-binding


Mass: 23714.400 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Details (production host): phoA promoter / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 1582 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#8: Chemical ChemComp-ACE / ACETYL GROUP / Acetyl group


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1556 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 8000, 0.1 M MES, 0.5 % n-Dodecyl-N,N-Dimethylamine-N-Oxide (LDAO)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→117.5 Å / Num. obs: 228060 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 37.88 Å2 / Rmerge(I) obs: 0.155 / Net I/σ(I): 7.6
Reflection shellResolution: 2→2.2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.997 / Mean I/σ(I) obs: 1.76 / % possible all: 84.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PGF
Resolution: 2→117.5 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.764 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.258 11412 5 %RANDOM
Rwork0.224 ---
obs0.226 216648 93.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→117.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20011 0 156 1556 21723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0220624
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213778
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.95828012
X-RAY DIFFRACTIONr_angle_other_deg0.7763.00333677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2252631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22424.121762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.927153243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9921574
X-RAY DIFFRACTIONr_chiral_restr0.0690.23183
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02122808
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024110
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 644 -
Rwork0.387 12050 -
obs--72.39 %

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