[English] 日本語
Yorodumi
- PDB-4rv0: Crystal structure of TN complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rv0
TitleCrystal structure of TN complex
Components
  • Nuclear protein localization protein 4 homolog
  • Transitional endoplasmic reticulum ATPase TER94
KeywordsPROTEIN BINDING / TRANSPORT PROTEIN / Ter94/p97 / Npl4 / AAA ATPase
Function / homology
Function and homology information


HSF1 activation / K11-linked polyubiquitin modification-dependent protein binding / larval midgut cell programmed cell death / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ovarian tumor domain proteases / Translesion Synthesis by POLH / ABC-family proteins mediated transport / Hedgehog ligand biogenesis / fusome / regulation of pole plasm oskar mRNA localization ...HSF1 activation / K11-linked polyubiquitin modification-dependent protein binding / larval midgut cell programmed cell death / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ovarian tumor domain proteases / Translesion Synthesis by POLH / ABC-family proteins mediated transport / Hedgehog ligand biogenesis / fusome / regulation of pole plasm oskar mRNA localization / endoplasmic reticulum membrane fusion / pole cell formation / Neutrophil degranulation / P granule / endoplasmic reticulum organization / vesicle-fusing ATPase / dendrite morphogenesis / autolysosome / muscle cell cellular homeostasis / oogenesis / lysosome organization / Golgi organization / autophagosome maturation / negative regulation of smoothened signaling pathway / regulation of neuron apoptotic process / proteasome complex / ubiquitin binding / negative regulation of canonical Wnt signaling pathway / microtubule cytoskeleton organization / cellular response to virus / positive regulation of neuron apoptotic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear membrane / positive regulation of viral entry into host cell / hydrolase activity / ubiquitin protein ligase binding / proteolysis / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Nuclear pore localisation protein Npl4, ubiquitin-like domain / Nuclear pore localisation protein NPL4 / NPL4, zinc-binding putative / Nuclear protein localization protein 4 / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / NPL4 family / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Vps4 oligomerisation, C-terminal ...Nuclear pore localisation protein Npl4, ubiquitin-like domain / Nuclear pore localisation protein NPL4 / NPL4, zinc-binding putative / Nuclear protein localization protein 4 / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / NPL4 family / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Vps4 oligomerisation, C-terminal / Vps4 C terminal oligomerisation domain / Barwin-like endoglucanases - #20 / Zinc finger domain / 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 / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / MPN domain / MPN domain profile. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ubiquitin-like domain superfamily / 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 TER94 / Nuclear protein localization protein 4 homolog / Nuclear protein localization protein 4 homolog
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.998 Å
AuthorsHao, Q. / Jiao, S. / Shi, Z.B. / Zhou, Z.C.
CitationJournal: To be Published
Title: Crystal structure of TN complex
Authors: Hao, Q. / Jiao, S. / Shi, Z.B. / Zhou, Z.C.
History
DepositionNov 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase TER94
B: Nuclear protein localization protein 4 homolog
C: Transitional endoplasmic reticulum ATPase TER94
D: Nuclear protein localization protein 4 homolog
E: Transitional endoplasmic reticulum ATPase TER94
F: Nuclear protein localization protein 4 homolog
G: Transitional endoplasmic reticulum ATPase TER94
H: Nuclear protein localization protein 4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,00415
Polymers115,3328
Non-polymers6727
Water18,8441046
1
A: Transitional endoplasmic reticulum ATPase TER94
B: Nuclear protein localization protein 4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0254
Polymers28,8332
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Transitional endoplasmic reticulum ATPase TER94
D: Nuclear protein localization protein 4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0254
Polymers28,8332
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Transitional endoplasmic reticulum ATPase TER94
F: Nuclear protein localization protein 4 homolog


Theoretical massNumber of molelcules
Total (without water)28,8332
Polymers28,8332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Transitional endoplasmic reticulum ATPase TER94
H: Nuclear protein localization protein 4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1215
Polymers28,8332
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.146, 83.141, 162.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Transitional endoplasmic reticulum ATPase TER94 / Valosin-containing protein homolog


Mass: 19617.834 Da / Num. of mol.: 4 / Fragment: N domain, UNP residues 20-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG2331, TER94, VCP / Plasmid: HT-pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7KN62, vesicle-fusing ATPase
#2: Protein
Nuclear protein localization protein 4 homolog


Mass: 9215.136 Da / Num. of mol.: 4 / Fragment: UBD domain, UNP residues 1-77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG4673, Npl4 / Plasmid: HT-pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9VBP9-2, UniProt: Q9VBP9*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1046 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsENTITY 2 IS BASED ON ISOFORM 2 OF DATABASE NPL4_DROME (Q9VBP9-2)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 23% w/v polyethylene glycol 3350, 0.2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9791 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 18, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.998→50 Å / Num. all: 74276 / Num. obs: 74127 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.1 % / Biso Wilson estimate: 19.67 Å2 / Rmerge(I) obs: 0.16
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2.18 / Num. unique all: 3503 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
AutoSolphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.998→45.384 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 26.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 3725 5.04 %RANDOM
Rwork0.2082 ---
all0.2104 74272 --
obs0.2104 73967 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.8 Å2
Refinement stepCycle: LAST / Resolution: 1.998→45.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7272 0 35 1046 8353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087462
X-RAY DIFFRACTIONf_angle_d1.28110069
X-RAY DIFFRACTIONf_dihedral_angle_d14.292879
X-RAY DIFFRACTIONf_chiral_restr0.081150
X-RAY DIFFRACTIONf_plane_restr0.0061301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9983-2.02360.3281360.2794236692
2.0236-2.05020.27281250.2425257399
2.0502-2.07830.28941380.23652591100
2.0783-2.1080.2731340.21232563100
2.108-2.13940.27891300.22372600100
2.1394-2.17290.28191470.23332569100
2.1729-2.20850.3121360.25842548100
2.2085-2.24660.35871140.31232611100
2.2466-2.28740.38741400.28082579100
2.2874-2.33140.28331370.26052570100
2.3314-2.3790.29291440.20562603100
2.379-2.43070.27611410.20332595100
2.4307-2.48730.26221340.20172568100
2.4873-2.54950.26781340.19822595100
2.5495-2.61840.21971360.19972622100
2.6184-2.69540.30391470.19952600100
2.6954-2.78240.24531470.20812573100
2.7824-2.88190.26411320.20262625100
2.8819-2.99720.22881540.1972572100
2.9972-3.13360.25761160.20252629100
3.1336-3.29880.22431150.19462654100
3.2988-3.50540.21561440.19372628100
3.5054-3.77590.20581270.18222647100
3.7759-4.15560.22191520.17682641100
4.1556-4.75640.18181690.15912628100
4.7564-5.99040.24251420.19232696100
5.9904-45.39520.28531540.237279699

+
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