[English] 日本語
Yorodumi
- PDB-6hb3: Structure of Hgh1, crystal form II -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hb3
TitleStructure of Hgh1, crystal form II
ComponentsProtein HGH1
KeywordsCHAPERONE / solenoid protein / Armadillo repeat
Function / homology
Function and homology information


translation elongation factor binding / chaperone-mediated protein folding / nucleus / cytoplasm
Similarity search - Function
Protein HGH1 N-terminal / Protein HGH1 C-terminal / Protein Hgh1 / Domain of unknown function (DUF383) / Domain of unknown function (DUF384) / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsMoenkemeyer, L. / Klaips, C.L. / Balchin, D. / Koerner, R. / Hartl, F.U. / Bracher, A.
CitationJournal: Mol.Cell / Year: 2019
Title: Chaperone Function of Hgh1 in the Biogenesis of Eukaryotic Elongation Factor 2.
Authors: Monkemeyer, L. / Klaips, C.L. / Balchin, D. / Korner, R. / Hartl, F.U. / Bracher, A.
History
DepositionAug 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 17, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein HGH1
B: Protein HGH1
C: Protein HGH1
D: Protein HGH1


Theoretical massNumber of molelcules
Total (without water)167,5664
Polymers167,5664
Non-polymers00
Water00
1
A: Protein HGH1


Theoretical massNumber of molelcules
Total (without water)41,8911
Polymers41,8911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein HGH1


Theoretical massNumber of molelcules
Total (without water)41,8911
Polymers41,8911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein HGH1


Theoretical massNumber of molelcules
Total (without water)41,8911
Polymers41,8911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein HGH1


Theoretical massNumber of molelcules
Total (without water)41,8911
Polymers41,8911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)191.798, 69.643, 206.866
Angle α, β, γ (deg.)90.000, 93.750, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA0 - 3566 - 362
21GLUGLUBB0 - 3566 - 362
12GLYGLYAA0 - 3556 - 361
22GLYGLYCC0 - 3556 - 361
13PROPROAA0 - 3576 - 363
23PROPRODD0 - 3576 - 363
14GLYGLYBB-1 - 3555 - 361
24GLYGLYCC-1 - 3555 - 361
15GLUGLUBB0 - 3566 - 362
25GLUGLUDD0 - 3566 - 362
16GLYGLYCC0 - 3556 - 361
26GLYGLYDD0 - 3556 - 361

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Protein HGH1 / HMG1/2 protein homolog


Mass: 41891.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: HGH1, YGR187C, G7538 / Plasmid: pProEX-HtB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 (DE3) / References: UniProt: P48362

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.11 Å3/Da / Density % sol: 70.1 % / Mosaicity: 0.12 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 16% PEG-3350, 0.1 M Na3-citrate and 20 mM DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3→47.96 Å / Num. obs: 54838 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.066 / Rrim(I) all: 0.123 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.093.50.7721470442460.7930.4820.9131.595
12.72-47.963.40.02426077750.9990.0150.02935.598

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation47.96 Å3.2 Å

-
Processing

Software
NameVersionClassification
XDSVERSION January 10, 2014data reduction
Aimless0.1.27data scaling
MOLREP11.0.05phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU B: 35.422 / SU ML: 0.273 / SU R Cruickshank DPI: 0.9234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.923 / ESU R Free: 0.331
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2302 2790 5.1 %RANDOM
Rwork0.2197 ---
obs0.2202 52045 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 171.82 Å2 / Biso mean: 73.132 Å2 / Biso min: 40.79 Å2
Baniso -1Baniso -2Baniso -3
1--3.36 Å20 Å2-0.21 Å2
2--3.55 Å20 Å2
3----0.18 Å2
Refinement stepCycle: final / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11485 0 0 0 11485
Num. residues----1434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01911684
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211566
X-RAY DIFFRACTIONr_angle_refined_deg0.9541.99215767
X-RAY DIFFRACTIONr_angle_other_deg0.811326715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.75451430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62724.887532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.576152248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.681568
X-RAY DIFFRACTIONr_chiral_restr0.0570.21815
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02112905
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022459
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A241790.05
12B241790.05
21A241360.05
22C241360.05
31A242050.05
32D242050.05
41B243760.03
42C243760.03
51B240540.06
52D240540.06
61C240110.06
62D240110.06
LS refinement shellResolution: 3→3.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 178 -
Rwork0.37 3644 -
all-3822 -
obs--96.15 %
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)
11.85940.6088-1.19551.8664-0.77474.39760.0006-0.05680.04340.26340.01080.12250.3175-0.2058-0.01140.2290.02040.01390.0378-0.04660.221448.2584.42416.175
25.49440.6678-0.56860.6761-0.22631.0144-0.18360.9947-0.2122-0.08040.0065-0.0408-0.0654-0.04630.17710.348-0.01660.04950.4381-0.10250.219198.9637.816-27.619
36.0991-0.734-0.55460.63890.34560.7417-0.154-1.2294-0.2810.0825-0.05560.0532-0.04140.05720.20950.32780.03250.0650.51450.16510.2081-9.7793.534130.857
41.9465-0.6008-1.48351.79760.77424.1839-0.04370.0507-0.1064-0.25550.0907-0.03990.26830.1068-0.0470.218-0.05610.00540.03410.01420.206240.5760.16886.921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 357
2X-RAY DIFFRACTION2B-1 - 358
3X-RAY DIFFRACTION3C-1 - 356
4X-RAY DIFFRACTION4D0 - 357

+
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