[English] 日本語
Yorodumi
- PDB-2he4: The crystal structure of the second PDZ domain of human NHERF-2 (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2he4
TitleThe crystal structure of the second PDZ domain of human NHERF-2 (SLC9A3R2) interacting with a mode 1 PDZ binding motif
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF2
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Phosphorylation / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


type 2 metabotropic glutamate receptor binding / type 3 metabotropic glutamate receptor binding / endomembrane system / phosphatase binding / protein-membrane adaptor activity / protein localization to plasma membrane / beta-catenin binding / protein-containing complex assembly / cadherin binding / apical plasma membrane ...type 2 metabotropic glutamate receptor binding / type 3 metabotropic glutamate receptor binding / endomembrane system / phosphatase binding / protein-membrane adaptor activity / protein localization to plasma membrane / beta-catenin binding / protein-containing complex assembly / cadherin binding / apical plasma membrane / signaling receptor binding / focal adhesion / extracellular exosome / identical protein binding / nucleus / plasma membrane
Similarity search - Function
EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily ...EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / 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
Na(+)/H(+) exchange regulatory cofactor NHE-RF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsPapagrigoriou, E. / Elkins, J.M. / Berridge, G. / Gileady, O. / Colebrook, S. / Gileadi, C. / Salah, E. / Savitsky, P. / Pantic, N. / Gorrec, F. ...Papagrigoriou, E. / Elkins, J.M. / Berridge, G. / Gileady, O. / Colebrook, S. / Gileadi, C. / Salah, E. / Savitsky, P. / Pantic, N. / Gorrec, F. / Bunkoczi, G. / Weigelt, J. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. / Doyle, D.A. / Structural Genomics Consortium (SGC)
CitationJournal: Protein Sci. / Year: 2007
Title: Structure of PICK1 and other PDZ domains obtained with the help of self-binding C-terminal extensions.
Authors: Elkins, J.M. / Papagrigoriou, E. / Berridge, G. / Yang, X. / Phillips, C. / Gileadi, C. / Savitsky, P. / Doyle, D.A.
History
DepositionJun 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9932
Polymers9,9311
Non-polymers621
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.803, 37.677, 40.340
Angle α, β, γ (deg.)90.00, 97.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-100-

HOH

-
Components

#1: Protein Na(+)/H(+) exchange regulatory cofactor NHE-RF2 / NHERF-2 / Tyrosine kinase activator protein 1 / TKA-1 / SRY-interacting protein 1 / SIP- 1 / Solute ...NHERF-2 / Tyrosine kinase activator protein 1 / TKA-1 / SRY-interacting protein 1 / SIP- 1 / Solute carrier family 9 isoform A3 regulatory factor 2 / NHE3 kinase A regulatory protein E3KARP / Sodium-hydrogen exchanger regulatory factor 2


Mass: 9931.314 Da / Num. of mol.: 1 / Fragment: PDZ 2 Domain (Residues 147-230) / Mutation: D229G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A3R2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 Rosetta / References: UniProt: Q15599
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.82 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97646 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 6, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97646 Å / Relative weight: 1
ReflectionResolution: 1.45→39.97 Å / Num. all: 13265 / Num. obs: 13060 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 0.98 % / Rmerge(I) obs: 0.0385
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 0.98 % / Rmerge(I) obs: 0.1403 / Mean I/σ(I) obs: 6.45 / Num. unique all: 2349 / % possible all: 98

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1i92 and 1g9o

1i92

1g9o


Resolution: 1.45→39.97 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.089 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18003 641 4.9 %RANDOM
Rwork0.12965 ---
all0.13203 13060 --
obs0.13203 12418 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.015 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å20 Å21.34 Å2
2---1.13 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.45→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms719 0 4 117 840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021733
X-RAY DIFFRACTIONr_bond_other_d0.0030.02553
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.988987
X-RAY DIFFRACTIONr_angle_other_deg0.95731330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.535589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10921.11136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.6215134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5761513
X-RAY DIFFRACTIONr_chiral_restr0.0940.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02807
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02154
X-RAY DIFFRACTIONr_nbd_refined0.2170.2107
X-RAY DIFFRACTIONr_nbd_other0.1970.2570
X-RAY DIFFRACTIONr_nbtor_refined0.160.2346
X-RAY DIFFRACTIONr_nbtor_other0.0820.2456
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.290.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8163470
X-RAY DIFFRACTIONr_mcbond_other2.473182
X-RAY DIFFRACTIONr_mcangle_it4.6865732
X-RAY DIFFRACTIONr_scbond_it6.2738290
X-RAY DIFFRACTIONr_scangle_it8.62411255
X-RAY DIFFRACTIONr_rigid_bond_restr2.85131368
X-RAY DIFFRACTIONr_sphericity_free10.4183117
X-RAY DIFFRACTIONr_sphericity_bonded5.95431276
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 49 -
Rwork0.101 919 -
obs--98.17 %

+
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