[English] 日本語
Yorodumi
- PDB-6meq: PcdhgB3 EC1-4 in 50 mM HEPES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6meq
TitlePcdhgB3 EC1-4 in 50 mM HEPES
ComponentsProtocadherin gamma-B3
KeywordsCELL ADHESION / cell-adhesion / neuronal self-avoidance
Function / homology
Function and homology information


homophilic cell adhesion via plasma membrane adhesion molecules / nervous system development / cell adhesion / calcium ion binding / plasma membrane
Similarity search - Function
Cadherin, C-terminal catenin-binding domain / Cadherin C-terminal cytoplasmic tail, catenin-binding region / Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. ...Cadherin, C-terminal catenin-binding domain / Cadherin C-terminal cytoplasmic tail, catenin-binding region / Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protocadherin gamma-B3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNicoludis, J.M. / Gaudet, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis.
Authors: Nicoludis, J.M. / Green, A.G. / Walujkar, S. / May, E.J. / Sotomayor, M. / Marks, D.S. / Gaudet, R.
History
DepositionSep 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protocadherin gamma-B3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,30310
Polymers45,9421
Non-polymers3619
Water1,65792
1
A: Protocadherin gamma-B3
hetero molecules

A: Protocadherin gamma-B3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,60620
Polymers91,8842
Non-polymers72118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3860 Å2
ΔGint-98 kcal/mol
Surface area44280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.811, 162.912, 52.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-671-

HOH

21A-688-

HOH

-
Components

#1: Protein Protocadherin gamma-B3 / PCDH-gamma-B3


Mass: 45942.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCDHGB3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9Y5G1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50 mM HEPES pH7, 10% PEG 5000MME, 4% ethylene glycol

-
Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→49.919 Å / Num. obs: 11833 / % possible obs: 94.21 % / Redundancy: 5.2 % / Biso Wilson estimate: 75.67 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.1249 / Net I/σ(I): 10.02
Reflection shellResolution: 2.9→3.004 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13rc1_2961)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5k8r

5k8r


Resolution: 2.9→49.919 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.9
RfactorNum. reflection% reflection
Rfree0.2709 1181 9.98 %
Rwork0.2244 --
obs0.2291 11831 94.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→49.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3229 0 9 92 3330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0013287
X-RAY DIFFRACTIONf_angle_d0.3774469
X-RAY DIFFRACTIONf_dihedral_angle_d11.4862010
X-RAY DIFFRACTIONf_chiral_restr0.041518
X-RAY DIFFRACTIONf_plane_restr0.003596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9002-3.03220.471040.4055956X-RAY DIFFRACTION70
3.0322-3.1920.38341370.34151232X-RAY DIFFRACTION89
3.192-3.3920.37991500.29141391X-RAY DIFFRACTION99
3.392-3.65380.32321520.2721377X-RAY DIFFRACTION99
3.6538-4.02130.281550.23361402X-RAY DIFFRACTION99
4.0213-4.60290.23921590.19881393X-RAY DIFFRACTION99
4.6029-5.79780.20281580.18261425X-RAY DIFFRACTION99
5.7978-49.92680.24931660.19211474X-RAY DIFFRACTION98
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)
12.46811.7621.71223.56021.95047.4471-0.11370.0617-0.1945-0.2332-0.1219-0.04150.06070.1079-0.00010.8550.0581-0.09580.60650.01910.732145.113958.430732.1088
23.2569-0.685-0.96686.00692.40891.6372-0.12270.0443-0.27020.04170.1942-0.3031-0.04780.3931-0.00010.95510.08070.02180.7341-0.00680.606538.631724.54593.4028
32.0895-1.5454-1.50523.26313.31186.3710.0875-0.12350.09780.22320.1024-0.3094-0.16720.1751-01.03030.0228-0.01870.6089-0.02850.985550.369-17.9577-22.8084
42.4404-1.9974-0.22524.70944.27985.72150.12140.071-0.20180.1955-0.44190.04690.48850.09350.00010.9075-0.05250.14030.75420.08790.643658.1885-55.4152-53.111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 99 )
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 208 )
3X-RAY DIFFRACTION3chain 'A' and (resid 209 through 313 )
4X-RAY DIFFRACTION4chain 'A' and (resid 314 through 416 )

+
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