[English] 日本語
Yorodumi
- PDB-3h0x: Crystal structure of peptide-binding domain of Kar2 protein from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h0x
TitleCrystal structure of peptide-binding domain of Kar2 protein from Saccharomyces cerevisiae
Components78 kDa glucose-regulated protein homolog
KeywordsCHAPERONE / structural genomics / APC89502.3 / peptide binding / Kar2 / BiP / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / ATP-binding / Endoplasmic reticulum / Nucleotide-binding / Phosphoprotein / Stress response
Function / homology
Function and homology information


fungal-type cell wall beta-glucan biosynthetic process / detection of unfolded protein / luminal surveillance complex / ubiquitin-dependent glycoprotein ERAD pathway / karyogamy involved in conjugation with cellular fusion / protein localization to endoplasmic reticulum / endoplasmic reticulum chaperone complex / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation / post-translational protein targeting to membrane, translocation ...fungal-type cell wall beta-glucan biosynthetic process / detection of unfolded protein / luminal surveillance complex / ubiquitin-dependent glycoprotein ERAD pathway / karyogamy involved in conjugation with cellular fusion / protein localization to endoplasmic reticulum / endoplasmic reticulum chaperone complex / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / response to unfolded protein / : / endoplasmic reticulum unfolded protein response / protein folding chaperone / heat shock protein binding / ATP-dependent protein folding chaperone / unfolded protein binding / protein refolding / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Endoplasmic reticulum targeting sequence. / 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 ...Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Endoplasmic reticulum targeting sequence. / 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, nucleotide binding domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsOsipiuk, J. / Bigelow, L. / Gu, M. / Sahi, C. / Craig, E.A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of peptide-binding domain of Kar2 protein from Saccharomyces cerevisiae.
Authors: Osipiuk, J. / Bigelow, L. / Gu, M. / Sahi, C. / Craig, E.A. / Joachimiak, A.
History
DepositionApr 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 78 kDa glucose-regulated protein homolog


Theoretical massNumber of molelcules
Total (without water)16,4141
Polymers16,4141
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: 78 kDa glucose-regulated protein homolog

A: 78 kDa glucose-regulated protein homolog


Theoretical massNumber of molelcules
Total (without water)32,8272
Polymers32,8272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2390 Å2
ΔGint-10.2 kcal/mol
Surface area14880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.846, 103.113, 80.792
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsAUTHORS STATE THAT THE MONOMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE.

-
Components

#1: Protein 78 kDa glucose-regulated protein homolog / GRP 78 / Immunoglobulin heavy chain-binding protein homolog / BiP


Mass: 16413.590 Da / Num. of mol.: 1 / Fragment: Peptide-binding domain: UNP residues 438-586
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GRP78, J1248, KAR2, SSD1, YJL034W / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16474
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.17 M Ammonium acetate, 0.085 M Sodium citrate, 25.5% PEG 4000, 15% Glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2008
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.92→35.1 Å / Num. all: 13673 / Num. obs: 13673 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 42.9 Å2 / Rmerge(I) obs: 0.067 / Χ2: 1.245 / Net I/σ(I): 31.919
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2 / Num. unique all: 638 / Χ2: 1.015 / % possible all: 98.5

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0054refinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OP6

2op6


Resolution: 1.92→35.1 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 9.021 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.15 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23 676 5 %RANDOM
Rwork0.186 ---
all0.188 13646 --
obs0.188 13646 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.85 Å2 / Biso mean: 27.182 Å2 / Biso min: 13.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---0.54 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.92→35.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1134 0 0 120 1254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221210
X-RAY DIFFRACTIONr_bond_other_d0.0030.02832
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9951651
X-RAY DIFFRACTIONr_angle_other_deg0.86732081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6345169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.38926.650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49915240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.103156
X-RAY DIFFRACTIONr_chiral_restr0.0970.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211353
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02201
X-RAY DIFFRACTIONr_mcbond_it0.8761.5779
X-RAY DIFFRACTIONr_mcbond_other0.2351.5314
X-RAY DIFFRACTIONr_mcangle_it1.53721280
X-RAY DIFFRACTIONr_scbond_it2.4753431
X-RAY DIFFRACTIONr_scangle_it4.3394.5360
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 49 -
Rwork0.285 929 -
all-978 -
obs-978 98.79 %
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)
11.8692-0.74070.96662.691-0.30781.0236-0.0330.10550.1296-0.03620.0845-0.2849-0.07270.0183-0.05150.060.004-0.01310.0617-0.02130.09358.56849.71544.5716
20.65360.95310.45842.4965-2.616510.2810.01880.06380.1164-0.13560.05030.24480.35520.1539-0.06920.12410.0808-0.00810.0850.04440.0787-7.145216.63833.5403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A437 - 551
2X-RAY DIFFRACTION2A552 - 586

+
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