[English] 日本語
Yorodumi
- PDB-3q5j: Crystal structure of the amino-terminal domain of HSP90 from Leis... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q5j
TitleCrystal structure of the amino-terminal domain of HSP90 from Leishmania major, LMJF33.0312:M1-K213 in the presence of 17-DMAP-geldanamycin
ComponentsHeat shock protein 83-1Heat shock response
KeywordsCHAPERONE / SLEEPING SICKNESS / LEISHMANIA / HEAT SHOCK PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding ...ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases ...Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / 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
Chem-D1S / Heat shock protein 83-1
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsWernimont, A.K. / Tempel, W. / Lin, Y.H. / Hutchinson, A. / MacKenzie, F. / Fairlamb, A. / Cossar, D. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. ...Wernimont, A.K. / Tempel, W. / Lin, Y.H. / Hutchinson, A. / MacKenzie, F. / Fairlamb, A. / Cossar, D. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Ferguson, M.A.J. / Hui, R. / Pizarro, J.C. / Hills, T. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the amino-terminal domain of HSP90 from Leishmania major, LMJF33.0312:M1-K213 in the presence of 17-DMAP-geldanamycin.
Authors: Wernimont, A.K. / Tempel, W. / Lin, Y.H. / Hutchinson, A. / MacKenzie, F. / Fairlamb, A. / Cossar, D. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Authors: Wernimont, A.K. / Tempel, W. / Lin, Y.H. / Hutchinson, A. / MacKenzie, F. / Fairlamb, A. / Cossar, D. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Ferguson, M.A.J. / Hui, R. / Pizarro, J.C. / Hills, T.
History
DepositionDec 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 5, 2012Group: Database references / Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 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_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: Heat shock protein 83-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7412
Polymers26,1101
Non-polymers6311
Water64936
1
A: Heat shock protein 83-1
hetero molecules

A: Heat shock protein 83-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4824
Polymers52,2212
Non-polymers1,2622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area1280 Å2
ΔGint-9 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.730, 111.730, 48.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein Heat shock protein 83-1 / Heat shock response


Mass: 26110.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF33.0312 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4Q4I6
#2: Chemical ChemComp-D1S / (4E,6Z,8S,9S,10E,12S,13R,14S,16R)-19-{[3-(dimethylamino)propyl]amino}-13-hydroxy-8,14-dimethoxy-4,10,12,16-tetramethyl-3,20,22-trioxo-2-azabicyclo[16.3.1]docosa-1(21),4,6,10,18-pentaen-9-yl carbamate


Mass: 630.772 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H50N4O8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2.2 M Na Formate, 0.1 M Na Acetate, 1 mM 17-DMAP-GA, 4 mM MgCl2, 2 mM TCEP, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 17938 / Num. obs: 17723 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.077 / Χ2: 1.26 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.1-2.185.40.7161.4216820.79993.2
2.18-2.265.90.5812.0516960.82196.3
2.26-2.376.40.45617630.84498.6
2.37-2.496.90.37117590.90399.6
2.49-2.657.40.2717810.924100
2.65-2.857.50.18417871.039100
2.85-3.147.50.10717891.225100
3.14-3.597.40.07518141.624100
3.59-4.527.30.05617952.153100
4.52-307.10.04218571.88499.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
TNTrefinement
PDB_EXTRACT3.1data extraction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H80

3h80


Resolution: 2.1→29.65 Å / Cor.coef. Fo:Fc: 0.9492 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 873 5.06 %RANDOM
Rwork0.2024 ---
all0.2039 17458 --
obs0.2039 17266 --
Displacement parametersBiso max: 139.35 Å2 / Biso mean: 59.1102 Å2 / Biso min: 29.17 Å2
Baniso -1Baniso -2Baniso -3
1--2.7704 Å20 Å20 Å2
2---2.7704 Å20 Å2
3---5.5409 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 45 36 1639
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.06
X-RAY DIFFRACTIONt_bond_d0.01
LS refinement shellResolution: 2.1→2.22 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2314 119 5.16 %
Rwork0.2289 2187 -
all0.2291 2306 -
Refinement TLS params.Method: refined / Origin x: -6.3712 Å / Origin y: 20.7253 Å / Origin z: 2.3049 Å
111213212223313233
T-0.0859 Å20.0417 Å20.075 Å2--0.0149 Å20 Å2--0.1603 Å2
L1.9512 °2-0.242 °20.343 °2-3.7006 °20.4513 °2--0.8422 °2
S0.0258 Å °0.2505 Å °-0.0352 Å °-0.3828 Å °0.0233 Å °-0.4143 Å °0.0295 Å °0.3144 Å °-0.049 Å °

+
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