[English] 日本語
Yorodumi
- PDB-4j0b: Structure of mitochondrial Hsp90 (TRAP1) with ADP-BeF3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j0b
TitleStructure of mitochondrial Hsp90 (TRAP1) with ADP-BeF3
ComponentsTNF receptor-associated protein 1
KeywordsCHAPERONE / ATPase / ATP binding / Mitochondria / ATPase chaperone
Function / homology
Function and homology information


nucleic acid metabolic process / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / mitochondrial inner membrane / calcium ion binding / protein kinase binding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
Heat shock protein 90, C-terminal domain / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain ...Heat shock protein 90, C-terminal domain / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / : / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.352 Å
AuthorsPartridge, J.R. / Lavery, L.A. / Agard, D.A.
CitationJournal: Mol.Cell / Year: 2014
Title: Structural asymmetry in the closed state of mitochondrial Hsp90 (TRAP1) supports a two-step ATP hydrolysis mechanism.
Authors: Lavery, L.A. / Partridge, J.R. / Ramelot, T.A. / Elnatan, D. / Kennedy, M.A. / Agard, D.A.
History
DepositionJan 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Apr 3, 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 / 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_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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_asym_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.ptnr1_auth_asym_id / _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_asym_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_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: TNF receptor-associated protein 1
B: TNF receptor-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,28112
Polymers148,0102
Non-polymers1,27110
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13310 Å2
ΔGint-105 kcal/mol
Surface area53990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.779, 96.566, 124.977
Angle α, β, γ (deg.)90.00, 134.29, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-995-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein TNF receptor-associated protein 1 / Trap1 protein


Mass: 74004.938 Da / Num. of mol.: 2 / Fragment: UNP residues 73-719
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: trap1 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: A8WFV1

-
Non-polymers , 5 types, 197 molecules

#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18 % (v/v) PEG3350, 0.2 M sodium malonate pH 6.6, 20-36 M hexamine cobalt mixed 1:1 with TRAP1 protein at 1 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2011
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.35→45 Å / Num. all: 62614 / Num. obs: 62301 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 59.14 Å2 / Rsym value: 0.087 / Net I/σ(I): 18
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 6139 / Rsym value: 0.544 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
PHENIX(phenix.refine: dev_1278)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD
Starting model: SeMET derivative of TRAP1 ADP-BeF3

Resolution: 2.352→29.82 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 30.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 2030 3.26 %random
Rwork0.2051 ---
obs0.2065 62239 98.95 %-
all-62899 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.352→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9674 0 68 187 9929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099949
X-RAY DIFFRACTIONf_angle_d1.17413432
X-RAY DIFFRACTIONf_dihedral_angle_d15.6493776
X-RAY DIFFRACTIONf_chiral_restr0.0781492
X-RAY DIFFRACTIONf_plane_restr0.0051714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3517-2.40640.3121180.28923645X-RAY DIFFRACTION91
2.4064-2.46650.33561340.27883963X-RAY DIFFRACTION99
2.4665-2.53320.3751340.27323998X-RAY DIFFRACTION99
2.5332-2.60770.34411370.27624022X-RAY DIFFRACTION99
2.6077-2.69180.34551430.26353985X-RAY DIFFRACTION99
2.6918-2.7880.27321350.25784034X-RAY DIFFRACTION100
2.788-2.89950.33231320.2564054X-RAY DIFFRACTION100
2.8995-3.03130.27451300.24234043X-RAY DIFFRACTION100
3.0313-3.1910.31251380.24554054X-RAY DIFFRACTION100
3.191-3.39060.29431370.23624056X-RAY DIFFRACTION100
3.3906-3.6520.27441410.21964011X-RAY DIFFRACTION100
3.652-4.01870.22691340.1924083X-RAY DIFFRACTION100
4.0187-4.59840.22621400.17184068X-RAY DIFFRACTION99
4.5984-5.78660.21881400.18184045X-RAY DIFFRACTION100
5.7866-29.8220.19361370.17334148X-RAY DIFFRACTION99
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)
13.92480.4777-0.52442.0372-0.23721.24240.12020.32820.1183-0.0506-0.09060.3129-0.0105-0.1549-0.03140.42110.0343-0.00150.33540.01830.5041-5.3017-2.1015-58.7839
22.56380.91381.76051.60440.72467.9287-0.0627-0.16230.10150.1621-0.0693-0.2819-0.1246-0.09790.09710.44480.03570.00840.30360.05510.6864.861610.8601-32.1923
33.92892.48731.4295.27231.24716.2241-0.26280.37850.75470.6302-0.3408-0.7607-0.71890.80390.63680.8119-0.0974-0.36710.68970.17911.240426.057819.9197-12.8345
44.37753.1381-2.5354.9347-0.61591.9761-0.1485-0.2425-0.1785-0.0473-0.1872-0.8688-0.12550.41620.29140.69710.0497-0.2380.7852-0.07510.895333.19120.327310.6942
56.704-0.21750.02131.34360.02520.92440.04530.70710.3712-0.3209-0.1153-0.424-0.01070.1790.07090.50370.08080.17420.5550.08930.770322.6526-1.4791-65.2468
60.85170.3516-0.38272.5975-1.06295.8240.2146-0.05180.2460.035-0.10320.0452-0.1259-0.2394-0.11040.3985-0.02980.10770.4612-0.0870.849625.4109-14.8165-35.6265
74.7774-2.18521.14113.6415-2.06254.5269-0.2959-0.0812-0.24680.00470.3197-0.35690.3928-0.11690.02710.4691-0.00980.0520.4004-0.13160.611717.2598-25.2583-8.7488
83.86882.02181.71973.38171.61526.3554-0.056-0.46240.17670.3897-0.0707-0.1316-0.1946-0.3440.14820.58870.1454-0.06180.6132-0.09110.54610.9022-13.812613.6398
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A and resid 85:310
2X-RAY DIFFRACTION2Chain A and resid 311:472
3X-RAY DIFFRACTION3Chain A and resid 473:566
4X-RAY DIFFRACTION4Chain A and resid 567:717
5X-RAY DIFFRACTION5Chain B and resid 85:310
6X-RAY DIFFRACTION6Chain B and resid 311:472
7X-RAY DIFFRACTION7Chain B and resid 473:566
8X-RAY DIFFRACTION8Chain B and resid 567:717

+
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