[English] 日本語
Yorodumi
- PDB-5glf: Structural insights into the interaction of p97 N-terminal domain... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5glf
TitleStructural insights into the interaction of p97 N-terminal domain and SHP motif in Derlin-1 rhomboid pseudoprotease
Components
  • Derlin-1
  • Transitional endoplasmic reticulum ATPase
KeywordsHYDROLASE/TRANSPORT PROTEIN / BETA-BARREL / ATPASE / DERLIN1 SHP BOX UBIQUITIN / PHOSPHORYLATION / HYDROLASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


Derlin-1-VIMP complex / endoplasmic reticulum quality control compartment / signal recognition particle binding / : / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding ...Derlin-1-VIMP complex / endoplasmic reticulum quality control compartment / signal recognition particle binding / : / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / Derlin-1 retrotranslocation complex / protein-DNA covalent cross-linking repair / cytoplasm protein quality control / positive regulation of protein K63-linked deubiquitination / positive regulation of oxidative phosphorylation / : / aggresome assembly / mitotic spindle disassembly / deubiquitinase activator activity / regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / cellular response to misfolded protein / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / K48-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / stress granule disassembly / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / ubiquitin-specific protease binding / MHC class I protein binding / ubiquitin-like protein ligase binding / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome maturation / response to unfolded protein / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of hippo signaling / HSF1 activation / translesion synthesis / interstrand cross-link repair / ATP metabolic process / proteasomal protein catabolic process / Protein methylation / endoplasmic reticulum unfolded protein response / ERAD pathway / Attachment and Entry / lipid droplet / proteasome complex / viral genome replication / Josephin domain DUBs / positive regulation of protein ubiquitination / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / negative regulation of smoothened signaling pathway / macroautophagy / positive regulation of protein-containing complex assembly / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / establishment of protein localization / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / positive regulation of non-canonical NF-kappaB signal transduction / protein destabilization / ADP binding / ABC-family proteins mediated transport / autophagy / positive regulation of protein catabolic process / cytoplasmic stress granule / Aggrephagy / azurophil granule lumen / KEAP1-NFE2L2 pathway / Ovarian tumor domain proteases / positive regulation of canonical Wnt signaling pathway / late endosome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / signaling receptor activity / site of double-strand break / Neddylation / cellular response to heat / ATPase binding / protease binding / ubiquitin-dependent protein catabolic process / protein phosphatase binding / secretory granule lumen / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / Attachment and Entry / early endosome / protein ubiquitination / ciliary basal body / protein domain specific binding / DNA repair / intracellular membrane-bounded organelle
Similarity search - Function
Derlin / Der1-like family / Vcp-like ATPase; Chain A, domain 2 - #10 / Rhomboid-like superfamily / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain ...Derlin / Der1-like family / Vcp-like ATPase; Chain A, domain 2 - #10 / Rhomboid-like superfamily / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / : / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Transitional endoplasmic reticulum ATPase / Derlin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLim, J.J. / Lee, Y. / Yoon, S.Y. / Ly, T.T. / Kang, J.Y. / Youn, H.-S. / An, J.Y. / Lee, J.-G. / Park, K.R. / Kim, T.G. ...Lim, J.J. / Lee, Y. / Yoon, S.Y. / Ly, T.T. / Kang, J.Y. / Youn, H.-S. / An, J.Y. / Lee, J.-G. / Park, K.R. / Kim, T.G. / Yang, J.K. / Jun, Y. / Eom, S.H.
CitationJournal: FEBS Lett. / Year: 2016
Title: Structural insights into the interaction of human p97 N-terminal domain and SHP motif in Derlin-1 rhomboid pseudoprotease.
Authors: Lim, J.J. / Lee, Y. / Yoon, S.Y. / Ly, T.T. / Kang, J.Y. / Youn, H.S. / An, J.Y. / Lee, J.G. / Park, K.R. / Kim, T.G. / Yang, J.K. / Jun, Y. / Eom, S.H.
History
DepositionJul 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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_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: Transitional endoplasmic reticulum ATPase
B: Derlin-1
C: Transitional endoplasmic reticulum ATPase
D: Derlin-1
E: Transitional endoplasmic reticulum ATPase
F: Derlin-1
G: Transitional endoplasmic reticulum ATPase
H: Derlin-1


Theoretical massNumber of molelcules
Total (without water)89,2228
Polymers89,2228
Non-polymers00
Water7,350408
1
A: Transitional endoplasmic reticulum ATPase
B: Derlin-1


Theoretical massNumber of molelcules
Total (without water)22,3062
Polymers22,3062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-8 kcal/mol
Surface area9790 Å2
MethodPISA
2
C: Transitional endoplasmic reticulum ATPase
D: Derlin-1


Theoretical massNumber of molelcules
Total (without water)22,3062
Polymers22,3062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-7 kcal/mol
Surface area9920 Å2
MethodPISA
3
E: Transitional endoplasmic reticulum ATPase
F: Derlin-1


Theoretical massNumber of molelcules
Total (without water)22,3062
Polymers22,3062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-7 kcal/mol
Surface area9530 Å2
MethodPISA
4
G: Transitional endoplasmic reticulum ATPase
H: Derlin-1


Theoretical massNumber of molelcules
Total (without water)22,3062
Polymers22,3062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-8 kcal/mol
Surface area9460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.802, 74.402, 222.114
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14C
24E
15C
25G
16E
26G

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROARGARGAA23 - 1918 - 176
21PROPROARGARGCC23 - 1918 - 176
12ASNASNARGARGAA24 - 1919 - 176
22ASNASNARGARGEE24 - 1919 - 176
13PROPROILEILEAA23 - 1898 - 174
23PROPROILEILEGG23 - 1898 - 174
14ASNASNARGARGCC24 - 1919 - 176
24ASNASNARGARGEE24 - 1919 - 176
15PROPROILEILECC23 - 1898 - 174
25PROPROILEILEGG23 - 1898 - 174
16ASNASNILEILEEE24 - 1899 - 174
26ASNASNILEILEGG24 - 1899 - 174

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 20859.961 Da / Num. of mol.: 4 / Fragment: P97 N-TERMINAL DOMAIN (UNP RESIDUES 21-199)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Escherichia coli (E. coli) / References: UniProt: P55072, vesicle-fusing ATPase
#2: Protein/peptide
Derlin-1 / Degradation in endoplasmic reticulum protein 1 / DERtrin-1 / Der1-like protein 1


Mass: 1445.566 Da / Num. of mol.: 4 / Fragment: SHP BOX (UNP RESIDUES 239-250) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BUN8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.03 Å3/Da / Density % sol: 39.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, BIS-TRIS PH 6.5, 0.2M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 34582 / % possible obs: 98.9 % / Redundancy: 10 % / Net I/σ(I): 9.1
Reflection shellResolution: 2.25→2.29 Å

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0103refinement
HKL-2000data reduction
MOLREPdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ7

3qq7


Resolution: 2.25→42.97 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.739 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.392 / ESU R Free: 0.233 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1716 5 %RANDOM
Rwork0.189 ---
obs0.191 32415 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.25→42.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5763 0 0 408 6171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195862
X-RAY DIFFRACTIONr_bond_other_d0.0090.025800
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.9757906
X-RAY DIFFRACTIONr_angle_other_deg1.797313333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4355713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69723.262282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.357151075
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5521565
X-RAY DIFFRACTIONr_chiral_restr0.1040.2889
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216489
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021300
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9253.4262876
X-RAY DIFFRACTIONr_mcbond_other2.9243.4252875
X-RAY DIFFRACTIONr_mcangle_it4.4435.1173581
X-RAY DIFFRACTIONr_mcangle_other4.4445.1183582
X-RAY DIFFRACTIONr_scbond_it3.863.9512986
X-RAY DIFFRACTIONr_scbond_other3.8593.9522987
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0325.7244326
X-RAY DIFFRACTIONr_long_range_B_refined8.52327.6876578
X-RAY DIFFRACTIONr_long_range_B_other8.46227.5526487
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A207800.13
12C207800.13
21A209300.12
22E209300.12
31A206320.12
32G206320.12
41C206060.13
42E206060.13
51C203760.14
52G203760.14
61E206360.12
62G206360.12
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 89 -
Rwork0.216 2129 -
obs--86.4 %

+
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