[English] 日本語
Yorodumi
- PDB-5fpm: Structure of heat shock-related 70kDA protein 2 with small-molecu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fpm
TitleStructure of heat shock-related 70kDA protein 2 with small-molecule ligand 5-phenyl-1,3,4-oxadiazole-2-thiol (AT809) in an alternate binding site.
ComponentsHEAT SHOCK-RELATED 70KDA PROTEIN 2
KeywordsCHAPERONE / HEAT SHOCK-RELATED PROTEIN / HEAT SHOCK / HSP70 / HSPA2 / PROTEIN-LIGAND COMPLEX / FRAGMENT SCREENING / ALTERNATE BINDING SITE / AT809.
Function / homology
Function and homology information


CatSper complex / glycolipid binding / synaptonemal complex disassembly / negative regulation of inclusion body assembly / male meiotic nuclear division / synaptonemal complex / meiotic spindle / male meiosis I / chaperone cofactor-dependent protein refolding / response to unfolded protein ...CatSper complex / glycolipid binding / synaptonemal complex disassembly / negative regulation of inclusion body assembly / male meiotic nuclear division / synaptonemal complex / meiotic spindle / male meiosis I / chaperone cofactor-dependent protein refolding / response to unfolded protein / spermatid development / Regulation of HSF1-mediated heat shock response / Attenuation phase / protein folding chaperone / heat shock protein binding / positive regulation of G2/M transition of mitotic cell cycle / Meiotic synapsis / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cold / male germ cell nucleus / ATP-dependent protein folding chaperone / tau protein binding / PKR-mediated signaling / disordered domain specific binding / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / spermatogenesis / blood microparticle / positive regulation of protein phosphorylation / enzyme binding / cell surface / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 ...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
5-PHENYL-1,3,4-OXADIAZOLE-2-THIOL / Heat shock-related 70 kDa protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsJhoti, H. / Ludlow, R.F. / Patel, S. / Saini, H.K. / Tickle, I.J. / Verdonk, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Detection of Secondary Binding Sites in Proteins Using Fragment Screening.
Authors: Ludlow, R.F. / Verdonk, M.L. / Saini, H.K. / Tickle, I.J. / Jhoti, H.
History
DepositionDec 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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-RELATED 70KDA PROTEIN 2
B: HEAT SHOCK-RELATED 70KDA PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1224
Polymers84,7662
Non-polymers3562
Water19,6901093
1
A: HEAT SHOCK-RELATED 70KDA PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5612
Polymers42,3831
Non-polymers1781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HEAT SHOCK-RELATED 70KDA PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5612
Polymers42,3831
Non-polymers1781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.860, 94.960, 81.540
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99999, 0.00174, 0.00515), (0.00169, -0.99995, 0.00959), (0.00517, -0.00958, -0.99994)
Vector: 24.189, -9.257, 40.724)

-
Components

#1: Protein HEAT SHOCK-RELATED 70KDA PROTEIN 2


Mass: 42383.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P54652
#2: Chemical ChemComp-IWT / 5-PHENYL-1,3,4-OXADIAZOLE-2-THIOL


Mass: 178.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6N2OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1093 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details5-PHENYL-1,3,4-OXADIAZOLE-2-THIOL (IWT): ASTEX COMPOUND REGISTRY AT809.
Sequence details3 EXTRA RESIDUES AT N TERM ARE REMAINS OF HIS TAG AFTER THROMBIN CLEAVAGE. RESIDUES 2-3 DELETED. ...3 EXTRA RESIDUES AT N TERM ARE REMAINS OF HIS TAG AFTER THROMBIN CLEAVAGE. RESIDUES 2-3 DELETED. RESIDUES 386-639 DELETED.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.14 % / Description: NONE
Crystal growpH: 8
Details: 1.0M NACL, 0.1M TRIS/HCL PH=8, 20.0% W/V PEG 8000. PROTEIN CONC. = 11MG/ML.

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU SATURN CCD / Detector: CCD / Date: Jun 24, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→38.4 Å / Num. obs: 53541 / % possible obs: 97.8 % / Observed criterion σ(I): -3.7 / Redundancy: 2.2 % / Biso Wilson estimate: 24.64 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.9
Reflection shellResolution: 1.96→2.03 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.9 / % possible all: 89.3

-
Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
MOSFLMdata reduction
SCALAdata scaling
CSEARCHphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FPD

5fpd


Resolution: 1.96→38.37 Å / Cor.coef. Fo:Fc: 0.9491 / Cor.coef. Fo:Fc free: 0.9282 / SU R Cruickshank DPI: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.206 / SU Rfree Blow DPI: 0.166 / SU Rfree Cruickshank DPI: 0.156
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 2660 5.08 %RANDOM
Rwork0.1695 ---
obs0.172 52336 97.63 %-
Displacement parametersBiso mean: 26.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.1137 Å20 Å20.4079 Å2
2---0.1682 Å20 Å2
3----1.9455 Å2
Refine analyzeLuzzati coordinate error obs: 0.191 Å
Refinement stepCycle: LAST / Resolution: 1.96→38.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5776 0 24 1093 6893
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125904HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.037982HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2068SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes155HARMONIC2
X-RAY DIFFRACTIONt_gen_planes890HARMONIC16
X-RAY DIFFRACTIONt_it5904HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.6
X-RAY DIFFRACTIONt_other_torsion15.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion803SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8099SEMIHARMONIC4
LS refinement shellResolution: 1.96→2.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2385 147 4.37 %
Rwork0.1763 3220 -
all0.179 3367 -
obs--85.29 %
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)
11.5316-0.17450.33130.8735-0.31310.7546-0.013-0.0170.00670.02830.0044-0.05610.01980.04240.0086-0.03210.0126-0.017-0.0586-0.0017-0.052527.499-9.28132.716
21.15670.0090.56860.82650.07741.5827-0.05320.15910.2153-0.08530.00930.0099-0.04410.01140.0439-0.02510.0037-0.041-0.05840.04280.000715.46398.355-8.1831
32.82280.3532.11350.9890.13063-0.2275-0.31860.31360.0612-0.08970.1697-0.2516-0.22460.3172-0.02580.0313-0.0313-0.0573-0.02170.011625.013916.316519.0281
41.44590.1756-0.20810.8808-0.29220.7992-0.04250.0811-0.0371-0.01570.0098-0.0311-0.0470.00020.0327-0.0369-0.01560.003-0.0562-0.0083-0.060251.66230.10538.244
51.3674-0.7424-0.31591.15280.49531.6452-0.0471-0.1305-0.31190.11960.0270.17350.1037-0.04690.0201-0.0211-0.02150.0453-0.0670.03580.013639.6568-17.741248.7625
62.5110.583-1.20981.1409-0.19991.8628-0.15550.2178-0.0951-0.0856-0.01860.04460.0953-0.07530.1741-0.0154-0.0131-0.0128-0.0573-0.0038-0.004549.3237-25.228721.8448

+
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