[English] 日本語
Yorodumi
- PDB-4xh2: Crystal structure of human paxillin LD4 motif in complex with Fab... -

+
Open data


ID or keywords:

Loading...

-
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 / endothelial cell migration / Smooth Muscle Contraction / 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 / endothelial cell migration / Smooth Muscle Contraction / GAB1 signalosome / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / stress fiber / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / beta-catenin binding / cellular response to reactive oxygen species / VEGFA-VEGFR2 Pathway / cell-cell junction / cell migration / lamellipodium / cell cortex / protein phosphatase binding / cell adhesion / focal adhesion / signal transduction / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Paxillin / : / : / Paxillin family / 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 ...Paxillin / : / : / Paxillin family / 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
Revision 1.4Sep 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
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

-
Components

-
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

-
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
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)

-
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

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PGF

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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more