[English] 日本語
Yorodumi
- PDB-4cid: Structural insights into the N-terminus of the EHD2 ATPase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cid
TitleStructural insights into the N-terminus of the EHD2 ATPase
ComponentsEH DOMAIN-CONTAINING PROTEIN 2
KeywordsHYDROLASE / MECHANOCHEMICAL ATPASE / DYNAMIN SUPERFAMILY
Function / homology
Function and homology information


positive regulation of endocytic recycling / plasma membrane tubulation / Factors involved in megakaryocyte development and platelet production / endocytic recycling / cortical actin cytoskeleton organization / positive regulation of myoblast fusion / protein localization to plasma membrane / caveola / recycling endosome membrane / endocytosis ...positive regulation of endocytic recycling / plasma membrane tubulation / Factors involved in megakaryocyte development and platelet production / endocytic recycling / cortical actin cytoskeleton organization / positive regulation of myoblast fusion / protein localization to plasma membrane / caveola / recycling endosome membrane / endocytosis / hydrolase activity / protein domain specific binding / calcium ion binding / GTP binding / perinuclear region of cytoplasm / ATP binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Topoisomerase; domain 3 - #20 / EH domain-containing protein, N-terminal / Domain of unknown function DUF5600 / N-terminal EH-domain containing protein / Domain of unknown function (DUF5600) / Topoisomerase; domain 3 / EH domain / EH domain profile. / Eps15 homology domain / EH domain ...Topoisomerase; domain 3 - #20 / EH domain-containing protein, N-terminal / Domain of unknown function DUF5600 / N-terminal EH-domain containing protein / Domain of unknown function (DUF5600) / Topoisomerase; domain 3 / EH domain / EH domain profile. / Eps15 homology domain / EH domain / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / EH domain-containing protein 2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsShah, C. / Daumke, O.
CitationJournal: Structure / Year: 2014
Title: Structural Insights Into Membrane Interaction and Caveolar Targeting of Dynamin-Like Ehd2.
Authors: Shah, C. / Hegde, B.G. / Mor, B. / Behrmann, E. / Mielke, T. / Moenke, G. / Spahn, C.M. / Lundmark, R. / Daumke, O. / Langen, R.
History
DepositionDec 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Dec 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EH DOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2134
Polymers62,6421
Non-polymers5713
Water724
1
A: EH DOMAIN-CONTAINING PROTEIN 2
hetero molecules

A: EH DOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4268
Polymers125,2852
Non-polymers1,1416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area8220 Å2
ΔGint-68 kcal/mol
Surface area48440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.851, 134.653, 56.068
Angle α, β, γ (deg.)90.00, 106.05, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein EH DOMAIN-CONTAINING PROTEIN 2


Mass: 62642.273 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PSKB2-LNB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q8BH64, dynamin GTPase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 58 %
Description: DATA COLLECTION STATISTICS ARE FOR THE ANOMALOUS DATA. EXPERIMENTAL (SEMET-DERIVED) PHASES DEPOSITED.
Crystal growpH: 6.5 / Details: 100 MM MES PH 6.5, 20 MM MGCL2, 4% PEG3350, 5% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97969
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97969 Å / Relative weight: 1
ReflectionResolution: 3→41 Å / Num. obs: 26426 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 1.63 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.5
Reflection shellResolution: 3→3.1 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.8 / % possible all: 98

-
Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
SHARPphasing
REFMACphasing
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QPT

2qpt


Resolution: 3→78.15 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.904 / SU B: 53.277 / SU ML: 0.429 / Cross valid method: THROUGHOUT / ESU R Free: 0.467
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES HAVE BEEN ADDED WITH TLS. EXPERIMENTAL (SEMET-DERIVED) PHASES USED FOR REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.27917 699 4.9 %RANDOM
Rwork0.23019 ---
obs0.23255 13424 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.356 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å2-0.41 Å2
2---2.28 Å20 Å2
3---1.22 Å2
Refinement stepCycle: LAST / Resolution: 3→78.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3956 0 33 4 3993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194075
X-RAY DIFFRACTIONr_bond_other_d0.0010.023980
X-RAY DIFFRACTIONr_angle_refined_deg1.0272.0015507
X-RAY DIFFRACTIONr_angle_other_deg0.71839176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3735492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27723.743179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1215688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5951528
X-RAY DIFFRACTIONr_chiral_restr0.0530.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214477
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02904
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_it1.6746.2861983
X-RAY DIFFRACTIONr_mcbond_other1.6746.2861982
X-RAY DIFFRACTIONr_mcangle_it2.9359.4152470
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7956.482091
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: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 57 -
Rwork0.337 989 -
obs--99.81 %
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)
13.22560.59073.24060.33970.95763.8355-0.4543-0.37790.34540.36230.13330.07870.249-0.06430.3211.01580.2668-0.01720.5552-0.0650.40332.6932-43.63320.5781
21.79730.72720.43911.12230.01470.8830.1330.0225-0.04670.3911-0.0383-0.0036-0.1586-0.0855-0.09470.2375-0.01870.08220.1112-0.030.078517.7646-52.0214-9.7448
31.6338-0.3581-0.59272.89171.95091.5213-0.21780.0078-0.2007-0.4620.2799-0.0791-0.2603-0.0058-0.06210.2034-0.10410.04920.35450.06470.051133.3236-26.6832-16.2083
44.36254.78151.142211.59952.32810.482-0.27390.27290.4033-0.58820.2230.0597-0.11350.05250.05090.19940.0060.0530.1814-0.02420.214330.2159-68.6141-15.5103
52.9192-0.2271.44553.02910.68063.24810.16970.2729-0.0093-0.0718-0.1667-0.10530.14060.0236-0.0030.07980.0120.0330.18810.02340.04930.4948-85.0038-43.2722
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A57 - 114
3X-RAY DIFFRACTION2A126 - 286
4X-RAY DIFFRACTION3A17 - 56
5X-RAY DIFFRACTION3A287 - 403
6X-RAY DIFFRACTION4A404 - 423
7X-RAY DIFFRACTION5A441 - 539

+
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