[English] 日本語
Yorodumi
- PDB-4hwc: Structure of ATBAG1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hwc
TitleStructure of ATBAG1
ComponentsBAG family molecular chaperone regulator 1
KeywordsAPOPTOSIS / three helix bundle / co-chaperone
Function / homology
Function and homology information


cytoplasm protein quality control by the ubiquitin-proteasome system / protein-folding chaperone binding / mitochondrion / nucleus / cytosol
Similarity search - Function
BAG domain / BAG domain superfamily / Molecular chaperone regulator BAG / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ubiquitin-like domain / Ubiquitin domain profile. ...BAG domain / BAG domain superfamily / Molecular chaperone regulator BAG / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BAG family molecular chaperone regulator 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsShen, Y. / Fang, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural insight into plant programmed cell death mediated by BAG proteins in Arabidopsis thaliana.
Authors: Fang, S. / Li, L. / Cui, B. / Men, S. / Shen, Y. / Yang, X.
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Feb 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: BAG family molecular chaperone regulator 1
B: BAG family molecular chaperone regulator 1
C: BAG family molecular chaperone regulator 1
D: BAG family molecular chaperone regulator 1
E: BAG family molecular chaperone regulator 1
F: BAG family molecular chaperone regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4298
Polymers58,3586
Non-polymers712
Water9,782543
1
A: BAG family molecular chaperone regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7622
Polymers9,7261
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BAG family molecular chaperone regulator 1


Theoretical massNumber of molelcules
Total (without water)9,7261
Polymers9,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BAG family molecular chaperone regulator 1


Theoretical massNumber of molelcules
Total (without water)9,7261
Polymers9,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BAG family molecular chaperone regulator 1


Theoretical massNumber of molelcules
Total (without water)9,7261
Polymers9,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: BAG family molecular chaperone regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7622
Polymers9,7261
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: BAG family molecular chaperone regulator 1


Theoretical massNumber of molelcules
Total (without water)9,7261
Polymers9,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.716, 96.847, 103.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
BAG family molecular chaperone regulator 1 / Bcl-2-associated athanogene 1


Mass: 9726.405 Da / Num. of mol.: 6 / Fragment: BAG domain (UNP residues 157-241)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g52060, BAG1, MSG15.15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0WUQ1
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 32% PEG3350, 0.2 M sodium chloride, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 3, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97911
ReflectionResolution: 1.798→35.478 Å / Num. all: 53532 / Num. obs: 53074 / % possible obs: 96.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.798→1.86 Å / % possible all: 96.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(PHENIX.REFINE)model building
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.798→35.478 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2514 2628 5.1 %
Rwork0.2382 --
obs0.2389 51507 96.28 %
all-53148 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.878 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2219 Å20 Å2-0 Å2
2--1.3387 Å20 Å2
3----2.5607 Å2
Refinement stepCycle: LAST / Resolution: 1.798→35.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3862 0 2 543 4407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063868
X-RAY DIFFRACTIONf_angle_d0.9595180
X-RAY DIFFRACTIONf_dihedral_angle_d13.7181494
X-RAY DIFFRACTIONf_chiral_restr0.076656
X-RAY DIFFRACTIONf_plane_restr0.003644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.798-1.8310.39491110.35352074X-RAY DIFFRACTION78
1.831-1.86620.31111190.34172282X-RAY DIFFRACTION87
1.8662-1.90430.35721300.29952387X-RAY DIFFRACTION90
1.9043-1.94570.31511350.26762448X-RAY DIFFRACTION93
1.9457-1.9910.29241440.26722502X-RAY DIFFRACTION95
1.991-2.04080.25831310.24092554X-RAY DIFFRACTION96
2.0408-2.09590.24231430.25952574X-RAY DIFFRACTION98
2.0959-2.15760.25671230.23662622X-RAY DIFFRACTION98
2.1576-2.22720.23831320.24252613X-RAY DIFFRACTION99
2.2272-2.30680.23591470.22772623X-RAY DIFFRACTION99
2.3068-2.39920.26291620.22492629X-RAY DIFFRACTION99
2.3992-2.50830.24461420.22072618X-RAY DIFFRACTION99
2.5083-2.64050.24851510.24082639X-RAY DIFFRACTION99
2.6405-2.80590.26571530.26332660X-RAY DIFFRACTION100
2.8059-3.02250.26171240.25132706X-RAY DIFFRACTION100
3.0225-3.32640.24241330.2342706X-RAY DIFFRACTION100
3.3264-3.80730.22831480.21722713X-RAY DIFFRACTION100
3.8073-4.79490.19151480.19882731X-RAY DIFFRACTION100
4.7949-35.4850.28361520.24512798X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -10.7535 Å / Origin y: -24.4369 Å / Origin z: 26.206 Å
111213212223313233
T0.0913 Å20.008 Å2-0.0126 Å2-0.0702 Å2-0.0164 Å2--0.105 Å2
L0.0649 °2-0.013 °2-0.0294 °2-0.0554 °20.007 °2--0.2014 °2
S0.0112 Å °-0.0061 Å °-0.0151 Å °-0.0229 Å °-0.0147 Å °0.0313 Å °-0.0029 Å °0.0247 Å °0.0032 Å °
Refinement TLS groupSelection details: all

+
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