[English] 日本語
Yorodumi
- PDB-4mtf: Structural Basis of Ca2+ Selectivity of a Voltage-gated Calcium C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mtf
TitleStructural Basis of Ca2+ Selectivity of a Voltage-gated Calcium Channel
ComponentsIon transport protein
KeywordsMETAL TRANSPORT / Tetrameric / Voltage-gated Ion Channel / Voltage-gated Calcium Channel / Calcium Selective / Transport protein / Membrane
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity / metal ion binding / identical protein binding
Similarity search - Function
Voltage-gated potassium channels. Chain C / Voltage-gated cation channel calcium and sodium / Helix Hairpins - #70 / Voltage-dependent channel domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTang, L. / Gamal El-Din, T.M. / Payandeh, J. / Martinez, G.Q. / Heard, T.M. / Scheuer, T. / Zheng, N. / Catterall, W.A.
CitationJournal: Nature / Year: 2014
Title: Structural basis for Ca2+ selectivity of a voltage-gated calcium channel.
Authors: Tang, L. / Gamal El-Din, T.M. / Payandeh, J. / Martinez, G.Q. / Heard, T.M. / Scheuer, T. / Zheng, N. / Catterall, W.A.
History
DepositionSep 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ion transport protein
B: Ion transport protein
C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,77422
Polymers109,8304
Non-polymers10,94318
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19550 Å2
ΔGint-188 kcal/mol
Surface area44290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.745, 177.790, 131.105
Angle α, β, γ (deg.)90.00, 132.69, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Ion transport protein


Mass: 27457.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (bacteria) / Strain: RM4018 / Gene: Abu_1752 / Plasmid: PFASTBAC DUAL / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: A8EVM5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.75
Details: 0.1M Na-citrate,pH4.75, 2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.75 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.75 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 45979 / Num. obs: 45979 / % possible obs: 93.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.094
Reflection shellResolution: 3.2→3.37 Å / % possible all: 99.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→29.9 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.894 / SU B: 14.558 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 0.581 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 2317 5 %RANDOM
Rwork0.24115 ---
obs0.24267 43661 93.24 %-
all-43661 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.726 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å2-0.72 Å2
2--3.14 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 3.2→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7192 0 190 4 7386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.027568
X-RAY DIFFRACTIONr_bond_other_d0.0050.027508
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9710276
X-RAY DIFFRACTIONr_angle_other_deg1.075317148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8345872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81521.781292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.535151236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2811540
X-RAY DIFFRACTIONr_chiral_restr0.0810.21224
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027980
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021860
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_it10.2049.943500
X-RAY DIFFRACTIONr_mcbond_other10.1969.943499
X-RAY DIFFRACTIONr_mcangle_it15.5114.8714368
X-RAY DIFFRACTIONr_mcangle_other15.48614.8614369
X-RAY DIFFRACTIONr_scbond_it8.59410.2564068
X-RAY DIFFRACTIONr_scbond_other8.59210.2484069
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.03715.1585909
X-RAY DIFFRACTIONr_long_range_B_refined20.5993.17831676
X-RAY DIFFRACTIONr_long_range_B_other20.5993.17831677
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 185 -
Rwork0.339 3421 -
obs--99.89 %

+
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