[English] 日本語
Yorodumi
- PDB-2p32: Crystal structure of the C-terminal 10 kDa subdomain from C. eleg... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2p32
TitleCrystal structure of the C-terminal 10 kDa subdomain from C. elegans Hsp70
ComponentsHeat shock 70 kDa protein A
KeywordsCHAPERONE / Three-helix bundle
Function / homology
Function and homology information


Regulation of HSF1-mediated heat shock response / GABA synthesis, release, reuptake and degradation / mRNA Splicing - Major Pathway / Clathrin-mediated endocytosis / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1-dependent transactivation / Neutrophil degranulation / retrograde transport, endosome to Golgi / SRP-dependent cotranslational protein targeting to membrane, translocation / chaperone cofactor-dependent protein refolding ...Regulation of HSF1-mediated heat shock response / GABA synthesis, release, reuptake and degradation / mRNA Splicing - Major Pathway / Clathrin-mediated endocytosis / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1-dependent transactivation / Neutrophil degranulation / retrograde transport, endosome to Golgi / SRP-dependent cotranslational protein targeting to membrane, translocation / chaperone cofactor-dependent protein refolding / protein folding chaperone / heat shock protein binding / determination of adult lifespan / ATP-dependent protein folding chaperone / response to heat / protein refolding / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / ATPase, nucleotide binding domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Heat shock protein hsp-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWorrall, L.J. / Walkinshaw, M.D.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Crystal structure of the C-terminal three-helix bundle subdomain of C. elegans Hsp70.
Authors: Worrall, L.J. / Walkinshaw, M.D.
History
DepositionMar 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 21, 2024Group: 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat shock 70 kDa protein A
B: Heat shock 70 kDa protein A
C: Heat shock 70 kDa protein A
D: Heat shock 70 kDa protein A
E: Heat shock 70 kDa protein A
F: Heat shock 70 kDa protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,32012
Polymers77,7446
Non-polymers5766
Water00
1
A: Heat shock 70 kDa protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0532
Polymers12,9571
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Heat shock 70 kDa protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0532
Polymers12,9571
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Heat shock 70 kDa protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0532
Polymers12,9571
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Heat shock 70 kDa protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0532
Polymers12,9571
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: Heat shock 70 kDa protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0532
Polymers12,9571
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: Heat shock 70 kDa protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0532
Polymers12,9571
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-116 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.927, 138.927, 100.704
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1 / Auth seq-ID: 533 - 614 / Label seq-ID: 13 - 94

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
DetailsThe biological assembly is a monomer.

-
Components

#1: Protein
Heat shock 70 kDa protein A


Mass: 12957.294 Da / Num. of mol.: 6 / Fragment: C-terminal 10 kDa subdomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: hsp-1, hsp70a / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3) / References: UniProt: P09446
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 55% ammonium sulphate, 0.5% PEG 400, 0.1M sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 4, 2006 / Details: Mirrors
RadiationMonochromator: Si 111 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionRedundancy: 8.74 % / Number: 146865 / Rmerge(I) obs: 0.136 / D res high: 3.2 Å / D res low: 35.99 Å
ReflectionResolution: 3.2→36 Å / Num. all: 16809 / Num. obs: 16809 / % possible obs: 99.9 % / Redundancy: 8.7 % / Biso Wilson estimate: 103.1 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 12.9
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.936 / Mean I/σ(I) obs: 2 / Num. measured all: 11782 / Num. unique all: 2399 / Rsym value: 0.936 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
SCALACCP4_3.2.17data scaling
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.7data extraction
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Preliminary model built using data from a mercury derivative crystal solved using MAD

Resolution: 3.2→36 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.225 / SU B: 66.939 / SU ML: 0.443 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.473 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2819 820 5.052 %RANDOM
Rwork0.2684 ---
all0.269 16809 --
obs-16232 96.694 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 89.409 Å2
Baniso -1Baniso -2Baniso -3
1-1.749 Å20 Å20 Å2
2--1.749 Å20 Å2
3----3.497 Å2
Refinement stepCycle: LAST / Resolution: 3.2→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3972 0 30 0 4002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224056
X-RAY DIFFRACTIONr_bond_other_d0.0040.022838
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.9945436
X-RAY DIFFRACTIONr_angle_other_deg1.10937038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1725486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.45827.353204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.53815834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg33.938156
X-RAY DIFFRACTIONr_chiral_restr0.1380.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024386
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02654
X-RAY DIFFRACTIONr_nbd_refined0.2960.21448
X-RAY DIFFRACTIONr_nbd_other0.2040.23063
X-RAY DIFFRACTIONr_nbtor_refined0.2160.21979
X-RAY DIFFRACTIONr_nbtor_other0.10.22173
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2530.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2230.216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0830.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.26
X-RAY DIFFRACTIONr_mcbond_it0.51.52642
X-RAY DIFFRACTIONr_mcbond_other0.0891.5984
X-RAY DIFFRACTIONr_mcangle_it0.81523930
X-RAY DIFFRACTIONr_mcangle_other0.40923306
X-RAY DIFFRACTIONr_scbond_it1.02731752
X-RAY DIFFRACTIONr_scbond_other0.30632244
X-RAY DIFFRACTIONr_scangle_it1.7194.51506
X-RAY DIFFRACTIONr_scangle_other0.7834.53732
Refine LS restraints NCS

Ens-ID: 1 / Number: 1135 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDRmsTypeWeight
1A0.03TIGHT POSITIONAL0.05
2B0.03TIGHT POSITIONAL0.05
3C0.03TIGHT POSITIONAL0.05
4D0.03TIGHT POSITIONAL0.05
5E0.05TIGHT POSITIONAL0.05
6F0.03TIGHT POSITIONAL0.05
1A0.04TIGHT THERMAL0.5
2B0.04TIGHT THERMAL0.5
3C0.04TIGHT THERMAL0.5
4D0.04TIGHT THERMAL0.5
5E0.04TIGHT THERMAL0.5
6F0.04TIGHT THERMAL0.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allNum. reflection obs% reflection obs (%)
3.2-3.2830.44560.42811420.42811981142100
3.283-3.3720.393610.3811180.38111791118100
3.372-3.4690.333550.37110890.36911441089100
3.469-3.5740.432510.39410770.39611281077100
3.574-3.690.675420.6927560.692105875675.425
3.69-3.8180.455330.4417540.441105975474.315
3.818-3.9610.462520.4739360.473101093697.822
3.961-4.1210.302460.2279340.231980934100
4.121-4.3010.336430.1939030.199946903100
4.301-4.5080.172480.1618630.161911863100
4.508-4.7480.145350.1768210.174856821100
4.748-5.030.274430.1667850.171828785100
5.03-5.370.192490.1697270.17776727100
5.37-5.790.186410.1896860.189727686100
5.79-6.3260.199440.2056270.205671627100
6.326-7.0450.234340.2165820.217616582100
7.045-8.0840.18250.1695270.17552527100
8.084-9.7780.166260.1594600.1648746099.795
9.778-13.3450.225240.163690.164393369100
13.345-360.297120.3572560.354268256100
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)
16.436-2.17416.215110.0481-6.382315.85040.099-1.5032-0.56030.43610.00030.1873-0.1577-0.7478-0.0994-0.2183-0.0919-0.4181-0.52470.2135-0.29783.7257-35.203637.7124
29.92783.48016.88937.83344.335412.09430.32760.0233-0.63980.5519-0.73760.76750.2084-1.23850.41-0.2910.0809-0.4648-0.5028-0.1968-0.1496-12.6511-51.415713.7753
33.9906-1.68070.108320.64660.02476.29970.4496-0.2284-0.03570.48630.20350.9577-0.669-0.6152-0.6531-0.05760.0092-0.3123-0.6879-0.0461-0.4954-12.3187-18.295114.1748
46.72972.5365.860710.83456.496315.25760.18441.642-0.6384-0.4823-0.1297-0.0517-0.13440.7387-0.0547-0.23560.1089-0.4146-0.5565-0.226-0.3071-3.7532-35.2907-3.5765
59.4967-3.43046.25068.7123-4.406111.21280.2452-0.0848-0.5557-0.4711-0.6835-0.7920.17851.2010.4383-0.2819-0.0735-0.4487-0.52640.1847-0.164712.5233-51.407320.4186
64.96771.60020.297321.4836-0.90455.31630.35470.30380.0462-0.17050.2946-0.9692-0.76780.5709-0.64930.01390.0081-0.3131-0.68610.0573-0.484212.2844-18.318219.8055
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 533 - 614 / Label seq-ID: 13 - 94

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC
44DD
55EE
66FF

+
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://pdbjlvh1.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