[English] 日本語
Yorodumi
- PDB-6pmt: Structure of Mortalin-NBD with adenosine-5'-monophosphate and thi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pmt
TitleStructure of Mortalin-NBD with adenosine-5'-monophosphate and thiodiphosphate
ComponentsStress-70 protein, mitochondrial
KeywordsCHAPERONE / complex / ATPase
Function / homology
Function and homology information


negative regulation of hemopoiesis / MIB complex / negative regulation of hematopoietic stem cell differentiation / SAM complex / negative regulation of erythrocyte differentiation / TIM23 mitochondrial import inner membrane translocase complex / inner mitochondrial membrane organization / Cristae formation / Complex III assembly / Complex I biogenesis ...negative regulation of hemopoiesis / MIB complex / negative regulation of hematopoietic stem cell differentiation / SAM complex / negative regulation of erythrocyte differentiation / TIM23 mitochondrial import inner membrane translocase complex / inner mitochondrial membrane organization / Cristae formation / Complex III assembly / Complex I biogenesis / calcium import into the mitochondrion / Mitochondrial protein import / iron-sulfur cluster assembly / mitochondrial nucleoid / chaperone cofactor-dependent protein refolding / Regulation of HSF1-mediated heat shock response / heat shock protein binding / protein folding chaperone / Mitochondrial protein degradation / protein export from nucleus / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / erythrocyte differentiation / ATP-dependent protein folding chaperone / intracellular protein transport / regulation of erythrocyte differentiation / unfolded protein binding / protein refolding / mitochondrial inner membrane / mitochondrial matrix / positive regulation of apoptotic process / focal adhesion / ubiquitin protein ligase binding / negative regulation of apoptotic process / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / ATP binding / nucleus / cytoplasm
Similarity search - Function
Chaperone DnaK / Defensin A-like - #30 / Defensin A-like / 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 ...Chaperone DnaK / Defensin A-like - #30 / Defensin A-like / 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 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / TRIHYDROGEN THIODIPHOSPHATE / PHOSPHATE ION / Stress-70 protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMoseng, M.A. / Nix, J.C. / Page, R.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128595 United States
National Science Foundation (NSF, United States)MCB 15-52113 United States
CitationJournal: to be published
Title: Structure of the mortalin nucleotide binding domain in complex with adenosine monophosphate
Authors: Moseng, M.A. / Nix, J.C. / Page, R.C.
History
DepositionJul 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Stress-70 protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0514
Polymers41,4161
Non-polymers6353
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.829, 56.548, 141.363
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Stress-70 protein, mitochondrial / 75 kDa glucose-regulated protein / GRP-75 / Heat shock 70 kDa protein 9 / Mortalin / MOT / Peptide- ...75 kDa glucose-regulated protein / GRP-75 / Heat shock 70 kDa protein 9 / Mortalin / MOT / Peptide-binding protein 74 / PBP74


Mass: 41416.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA9, GRP75, HSPA9B, mt-HSP70 / Organ: HEART / Plasmid: pHis//2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: P38646
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-PIS / TRIHYDROGEN THIODIPHOSPHATE / THIOPYROPHOSPHATE


Mass: 193.033 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H3O6P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 100 mM sodium acetate, 20% (w/v) PEG 3000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000074 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000074 Å / Relative weight: 1
ReflectionResolution: 2.3→49.49 Å / Num. obs: 19382 / % possible obs: 98.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 22.01 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06631 / Rrim(I) all: 0.072 / Net I/σ(I): 21.78
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 0.1664 / Num. unique obs: 1811 / CC1/2: 0.98

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NHK

6nhk


Resolution: 2.3→49.486 Å / SU ML: 0.1992 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.2556
RfactorNum. reflection% reflection
Rfree0.2054 1928 9.94 %
Rwork0.1909 --
obs0.1924 19378 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.39 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 37 152 2948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822856
X-RAY DIFFRACTIONf_angle_d1.20873891
X-RAY DIFFRACTIONf_chiral_restr0.0605457
X-RAY DIFFRACTIONf_plane_restr0.0057512
X-RAY DIFFRACTIONf_dihedral_angle_d14.92211025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.22261200.20871168X-RAY DIFFRACTION93.06
2.33-2.360.28291330.21661179X-RAY DIFFRACTION93.45
2.36-2.40.25421520.21361178X-RAY DIFFRACTION94.33
2.4-2.430.21791230.21171228X-RAY DIFFRACTION97.97
2.43-2.470.2671530.20481239X-RAY DIFFRACTION99.07
2.47-2.510.25421110.21281264X-RAY DIFFRACTION99.13
2.51-2.550.23091430.20921262X-RAY DIFFRACTION99.65
2.55-2.60.261530.22441225X-RAY DIFFRACTION99.57
2.6-2.650.21961480.2061259X-RAY DIFFRACTION99.79
2.65-2.70.20161460.21681230X-RAY DIFFRACTION98.99
2.7-2.760.2321390.2131267X-RAY DIFFRACTION99.86
2.76-2.830.24891180.20411249X-RAY DIFFRACTION99.13
2.83-2.90.22151530.2121247X-RAY DIFFRACTION99.22
2.9-2.980.24731380.22011265X-RAY DIFFRACTION99.15
2.98-3.060.23981380.21451209X-RAY DIFFRACTION98.75
3.06-3.160.22521410.21171255X-RAY DIFFRACTION98.87
3.16-3.280.22541390.21441230X-RAY DIFFRACTION98.56
3.28-3.410.21311340.19931217X-RAY DIFFRACTION98.18
3.41-3.560.19761380.17911258X-RAY DIFFRACTION97.42
3.56-3.750.16821390.18351223X-RAY DIFFRACTION97.92
3.75-3.980.15331230.15971226X-RAY DIFFRACTION97.54
3.98-4.290.17311520.16111253X-RAY DIFFRACTION98.18
4.29-4.720.17881340.14641213X-RAY DIFFRACTION97.75
4.72-5.410.1611410.17051230X-RAY DIFFRACTION98.42
5.41-6.810.18151330.19271249X-RAY DIFFRACTION98.71
6.81-49.4860.16761300.16081250X-RAY DIFFRACTION98.57

+
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