[English] 日本語
Yorodumi
- PDB-3msv: The hypoxic regulator of sterol synthesis Nro1 is a nuclear impor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3msv
TitleThe hypoxic regulator of sterol synthesis Nro1 is a nuclear import adaptor
ComponentsNuclear import adaptor, Nro1
KeywordsPROTEIN BINDING / helix repeats / HEAT repeats
Function / homology
Function and homology information


positive regulation of SREBP signaling pathway / cation binding / SREBP signaling pathway / regulation of translation / cellular response to hypoxia / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Negative regulator of Ofd1/Enhancer of translation termination 1 / Nuclear pore complex subunit Nro1
Similarity search - Domain/homology
Negative regulator of ofd1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.18 Å
AuthorsYeh, T.L. / Amzel, L.M. / Bianchet, M.A.
CitationJournal: Structure / Year: 2011
Title: The hypoxic regulator of sterol synthesis nro1 is a nuclear import adaptor.
Authors: Yeh, T.L. / Lee, C.Y. / Amzel, L.M. / Espenshade, P.J. / Bianchet, M.A.
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nuclear import adaptor, Nro1
B: Nuclear import adaptor, Nro1


Theoretical massNumber of molelcules
Total (without water)88,9732
Polymers88,9732
Non-polymers00
Water7,116395
1
A: Nuclear import adaptor, Nro1


Theoretical massNumber of molelcules
Total (without water)44,4861
Polymers44,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear import adaptor, Nro1


Theoretical massNumber of molelcules
Total (without water)44,4861
Polymers44,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-4 kcal/mol
Surface area34000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.790, 107.960, 100.780
Angle α, β, γ (deg.)90.00, 102.60, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Nuclear import adaptor, Nro1


Mass: 44486.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPCC4B3.07 / Plasmid: pPROEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9USJ7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.3 M ammonium tartrate dibasic, 0.1 M Bis-TrisHCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.5

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU FR-E SUPERBRIGHT11.5418
SYNCHROTRONAPS 31-ID20.979
Detector
TypeIDDetectorDate
RIGAKU SATURN 9441CCDOct 20, 2008
RAYONIX MX225HE2CCDFeb 15, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.9791
ReflectionResolution: 2.18→19.73 Å / Num. all: 51980 / Num. obs: 51200 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.087 / Net I/σ(I): 12.9
Reflection shellResolution: 2.18→2.3 Å / Rmerge(I) obs: 0.515 / % possible all: 93.2

-
Processing

Software
NameVersionClassification
StructureStudiodata collection
SOLVEphasing
REFMAC5.5.0088refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.18→19.73 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9 / SU B: 5.602 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25701 2576 5 %RANDOM
Rwork0.20452 ---
obs0.2072 48602 98.61 %-
all-51200 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.783 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å2-0.31 Å2
2---0.56 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.18→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5630 0 0 395 6025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225750
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9687816
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6865699
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93725.695295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.297151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1221525
X-RAY DIFFRACTIONr_chiral_restr0.0880.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214375
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6851.53509
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33325662
X-RAY DIFFRACTIONr_scbond_it1.95232241
X-RAY DIFFRACTIONr_scangle_it3.244.52152
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.181→2.237 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 174 -
Rwork0.285 3112 -
obs--86.66 %

+
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