[English] 日本語
Yorodumi
- PDB-2uzc: Structure of human PDLIM5 in complex with the C-terminal peptide ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2uzc
TitleStructure of human PDLIM5 in complex with the C-terminal peptide of human alpha-actinin-1
ComponentsPDZ AND LIM DOMAIN 5
KeywordsSIGNALING PROTEIN / METAL-BINDING / ENIGMA HOMOLOG / PHOSPHORYLATION / LIM DOMAIN / PDZ DOMAIN
Function / homology
Function and homology information


muscle structure development / cell growth involved in cardiac muscle cell development / : / muscle alpha-actinin binding / cadherin binding involved in cell-cell adhesion / regulation of dendritic spine morphogenesis / actinin binding / Neurexins and neuroligins / regulation of synapse assembly / filamentous actin ...muscle structure development / cell growth involved in cardiac muscle cell development / : / muscle alpha-actinin binding / cadherin binding involved in cell-cell adhesion / regulation of dendritic spine morphogenesis / actinin binding / Neurexins and neuroligins / regulation of synapse assembly / filamentous actin / stress fiber / protein kinase C binding / cell projection / adherens junction / Z disc / actin cytoskeleton / presynapse / heart development / actin binding / actin cytoskeleton organization / postsynaptic density / membrane / metal ion binding / cytosol
Similarity search - Function
Domain of unknown function DUF4749 / Domain of unknown function (DUF4749) / 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. / PDZ domain / Pdz3 Domain / PDZ domain ...Domain of unknown function DUF4749 / Domain of unknown function (DUF4749) / 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. / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
PDZ and LIM domain protein 5 / PDZ and LIM domain protein 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBunkoczi, G. / Elkins, J. / Salah, E. / Burgess-Brown, N. / Papagrigoriou, E. / Pike, A.C.W. / Turnbull, A. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. ...Bunkoczi, G. / Elkins, J. / Salah, E. / Burgess-Brown, N. / Papagrigoriou, E. / Pike, A.C.W. / Turnbull, A. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Doyle, D.
CitationJournal: Protein Sci. / Year: 2010
Title: Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms.
Authors: Elkins, J.M. / Gileadi, C. / Shrestha, L. / Phillips, C. / Wang, J. / Muniz, J.R. / Doyle, D.A.
History
DepositionApr 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 28, 2015Group: Database references / Other
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PDZ AND LIM DOMAIN 5
B: PDZ AND LIM DOMAIN 5
C: PDZ AND LIM DOMAIN 5
D: PDZ AND LIM DOMAIN 5
E: PDZ AND LIM DOMAIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,92513
Polymers46,5885
Non-polymers3378
Water8,287460
1
A: PDZ AND LIM DOMAIN 5


Theoretical massNumber of molelcules
Total (without water)9,3181
Polymers9,3181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PDZ AND LIM DOMAIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4153
Polymers9,3181
Non-polymers982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PDZ AND LIM DOMAIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3532
Polymers9,3181
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: PDZ AND LIM DOMAIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4514
Polymers9,3181
Non-polymers1333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: PDZ AND LIM DOMAIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3883
Polymers9,3181
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.250, 36.474, 88.706
Angle α, β, γ (deg.)90.00, 99.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.71731, -0.6454, -0.26254), (0.5981, -0.76365, 0.24314), (-0.35741, 0.01738, 0.93378)20.2177, -15.0469, 22.95777
2given(-0.19437, 0.98072, 0.02022), (0.97218, 0.18985, 0.13717), (0.13068, 0.04632, -0.99034)-13.56198, -36.80161, 32.61575
3given(0.34988, 0.92298, -0.16026), (-0.91094, 0.2953, -0.28809), (-0.21857, 0.24678, 0.9441)6.8579, 12.03168, 39.62221
4given(0.67922, -0.65864, 0.32381), (-0.68185, -0.72953, -0.05365), (0.27157, -0.18435, -0.9446)-31.24924, -15.49909, 12.26183

-
Components

#1: Protein
PDZ AND LIM DOMAIN 5 / HUMAN PDLIM5


Mass: 9317.584 Da / Num. of mol.: 5 / Fragment: RESIDUES 1-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: Q8WVK0, UniProt: Q96HC4*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE LAST 4 RESIDUES WERE TAGGED TO THE C-TERMINUS TO PROMOTE CRYSTAL CONTACTS

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38 %
Crystal growDetails: 20% PEG3350 0.20 M KSCN

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 3, 2007 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→46.4 Å / Num. obs: 49917 / % possible obs: 79.7 % / Observed criterion σ(I): 0 / Redundancy: 2.69 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.2
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 0.83 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.98 / % possible all: 37

-
Processing

Software
NameVersionClassification
REFMAC5.3.0034refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PKT

2pkt


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.312 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2527 5.1 %RANDOM
Rwork0.163 ---
obs0.166 47380 79.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å2-0.56 Å2
2--0.72 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 14 460 3662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223346
X-RAY DIFFRACTIONr_bond_other_d0.0010.022235
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9644523
X-RAY DIFFRACTIONr_angle_other_deg0.9335519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.815437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92625.786140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65915591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0151517
X-RAY DIFFRACTIONr_chiral_restr0.0840.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023754
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02594
X-RAY DIFFRACTIONr_nbd_refined0.2040.2627
X-RAY DIFFRACTIONr_nbd_other0.1940.22313
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21572
X-RAY DIFFRACTIONr_nbtor_other0.0860.21874
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2310
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.16932257
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.253499
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.17881236
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.097111023
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.34 72
Rwork0.251 1339
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)
12.3815-0.5863-1.47320.5006-0.23282.12220.08450.11730.1840.13550.0102-0.0685-0.2794-0.1072-0.09470.0441-0.01980.0193-0.0552-0.006-0.04329.9072.9667-0.1126
22.10960.68941.04160.89640.32571.82620.0613-0.0393-0.19450.0893-0.0837-0.1714-0.0028-0.07080.0223-0.0283-0.0064-0.0028-0.06370.0008-0.000311.241-11.36319.1072
31.3577-0.09510.57170.51420.18820.8041-0.03740.0702-0.01240.00180.07420.0095-0.0020.0639-0.0368-0.0325-0.0060.0016-0.0068-0.007-0.0207-12.5631-26.538834.2257
41.46950.0226-0.70270.50640.00931.2075-0.0194-0.0584-0.00540.00130.0017-0.0563-0.04520.02980.0177-0.03150.0013-0.0072-0.0212-0.0108-0.013513.16073.749538.0767
52.6005-0.32020.13291.4375-0.66131.9360.0471-0.01460.0076-0.104-0.05810.0053-0.0676-0.21020.011-0.0360.025-0.0116-0.0224-0.0351-0.0465-26.4705-24.486114.6904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 87
2X-RAY DIFFRACTION2B0 - 87
3X-RAY DIFFRACTION3C0 - 87
4X-RAY DIFFRACTION4D0 - 87
5X-RAY DIFFRACTION5E0 - 87

+
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