[English] 日本語
Yorodumi
- PDB-5f5r: TRAP1N-ADPNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f5r
TitleTRAP1N-ADPNP
ComponentsHeat shock protein 75 kDa, mitochondrial
KeywordsCHAPERONE / ATPase / GHKL ATPase
Function / homology
Function and homology information


translational attenuation / negative regulation of cellular respiration / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / chaperone-mediated protein folding / negative regulation of reactive oxygen species biosynthetic process / cell periphery / ATP-dependent protein folding chaperone / mitochondrial intermembrane space ...translational attenuation / negative regulation of cellular respiration / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / chaperone-mediated protein folding / negative regulation of reactive oxygen species biosynthetic process / cell periphery / ATP-dependent protein folding chaperone / mitochondrial intermembrane space / unfolded protein binding / protein folding / mitochondrial inner membrane / mitochondrial matrix / protein kinase binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane
Similarity search - Function
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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase ...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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTsai, F.T.F. / Lee, S. / Sung, N. / Lee, J. / Chang, C. / Joachimiak, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM111084 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104980 United States
Welch FoundationQ-1530 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Mitochondrial Hsp90 is a ligand-activated molecular chaperone coupling ATP binding to dimer closure through a coiled-coil intermediate.
Authors: Sung, N. / Lee, J. / Kim, J.H. / Chang, C. / Joachimiak, A. / Lee, S. / Tsai, F.T.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat shock protein 75 kDa, mitochondrial
B: Heat shock protein 75 kDa, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1536
Polymers52,0922
Non-polymers1,0614
Water9,152508
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-24 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.570, 143.168, 103.011
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

21A-590-

HOH

31B-521-

HOH

41B-589-

HOH

51B-652-

HOH

-
Components

#1: Protein Heat shock protein 75 kDa, mitochondrial / HSP 75 / TNFR-associated protein 1 / Tumor necrosis factor type 1 receptor-associated protein / TRAP-1


Mass: 26046.145 Da / Num. of mol.: 2 / Fragment: UNP residues 60-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAP1, HSP75 / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12931
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 508 / 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: 3.46 Å3/Da / Density % sol: 64.45 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate pH 5.6, 22% PEG4000, 5% isopropanol

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.85→29.41 Å / Num. all: 54569 / Num. obs: 54569 / % possible obs: 98.5 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 8.4 / % possible all: 98

-
Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CG9

2cg9


Resolution: 1.85→29.41 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.623 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2899 5 %RANDOM
Rwork0.1757 ---
obs0.1771 54569 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.42 Å2 / Biso mean: 24.64 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 1.85→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3443 0 64 508 4015
Biso mean--2.81 20.47 -
Num. residues----447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0223560
X-RAY DIFFRACTIONr_angle_refined_deg0.6561.9774807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4775444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47724.211152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97315633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1161522
X-RAY DIFFRACTIONr_chiral_restr0.0480.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.022592
X-RAY DIFFRACTIONr_mcbond_it2.0721.52207
X-RAY DIFFRACTIONr_mcangle_it3.33723542
X-RAY DIFFRACTIONr_scbond_it5.05131353
X-RAY DIFFRACTIONr_scangle_it7.8614.51265
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 198 -
Rwork0.216 3803 -
all-4001 -
obs--93.94 %
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)
11.15250.95780.35952.809-0.25331.2776-0.00350.18540.067-0.3726-0.0751-0.23970.01270.20670.07850.1270.03370.11280.12510.040.1102-36.615255.701767.8599
21.02540.4577-0.10281.71670.37571.3488-0.04280.1935-0.123-0.21010.03360.0759-0.038-0.12510.00920.047-0.0059-0.040.0929-0.02680.0662-52.44515.645264.9082
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A70 - 294
2X-RAY DIFFRACTION2B70 - 294

+
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