[English] 日本語
Yorodumi
- SASDBW9: Immunoglobulin domains 4,5 of Nucleoporin Pom152 (Pom152 Ig-4,5: ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDBW9
SampleImmunoglobulin domains 4,5 of Nucleoporin Pom152 (Pom152 Ig-4,5: amino acids 718-920)
  • Nucleoporin POM152 (protein), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Function / homology
Function and homology information


nuclear pore transmembrane ring / spindle pole body duplication / nuclear pore organization / structural constituent of nuclear pore / nucleocytoplasmic transport / nuclear envelope lumen / mRNA transport / nuclear pore / protein-membrane adaptor activity / nuclear periphery ...nuclear pore transmembrane ring / spindle pole body duplication / nuclear pore organization / structural constituent of nuclear pore / nucleocytoplasmic transport / nuclear envelope lumen / mRNA transport / nuclear pore / protein-membrane adaptor activity / nuclear periphery / cell periphery / protein import into nucleus / nuclear envelope / nuclear membrane / mitochondrion
Similarity search - Function
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
CitationDate: 2017 Feb
Title: Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex
Authors: Upla P / Kim S / Sampathkumar P / Dutta K / Cahill S / Chemmama I / Williams R / Bonanno J / Rice W / Stokes D / Cowburn D / Almo S / Sali A / Rout M
Contact author
  • Seung Joong Kim (University of California, San Francisco (UCSF))

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #1109
Type: dummy / Software: DAMMIN / Radius of dummy atoms: 2.00 A / Chi-square value: 1.966
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Immunoglobulin domains 4,5 of Nucleoporin Pom152 (Pom152 Ig-4,5: amino acids 718-920)
Specimen concentration: 0.50-10.10
BufferName: 10mM HEPES, 150mM NaCl, 10%(v/v) glycerol, 5mM DTT / pH: 7.5
Entity #576Type: protein / Description: Nucleoporin POM152 / Formula weight: 23.805 / Num. of mol.: 1
Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P39685
Sequence: RVKPSASLKL HHDLKLCLGD HSSVPVALKG QGPFTLTYDI IETFSSKRKT FEIKEIKTNE YVIKTPVFTT GGDYILSLVS IKDSTGCVVG LSQPDAKIQV RRDIPSAAFN FFEPIKEAKI KHGSVTEIPL KLSGEGPFTV KFKHMDYDGN IVKEFENKFQ NSYKPALKVS ...Sequence:
RVKPSASLKL HHDLKLCLGD HSSVPVALKG QGPFTLTYDI IETFSSKRKT FEIKEIKTNE YVIKTPVFTT GGDYILSLVS IKDSTGCVVG LSQPDAKIQV RRDIPSAAFN FFEPIKEAKI KHGSVTEIPL KLSGEGPFTV KFKHMDYDGN IVKEFENKFQ NSYKPALKVS KEGLYQLVDI RDSSCQGNVI YRNSLYKVSF LEKEGHHHHH H

-
Experimental information

BeamInstrument name: Stanford Synchrotron Radiation Lightsource (SSRL) BL4-2
City: Stanford, CA / 国: USA / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.098 Å / Dist. spec. to detc.: 1.7 mm
DetectorName: Rayonix MX225-HE
Scan
Title: Immunoglobulin domains 4,5 of Nucleoporin Pom152 (Pom152 Ig-4,5: amino acids 718-920)
Measurement date: Apr 12, 2015 / Storage temperature: 15 °C / Cell temperature: 15 °C / Exposure time: 1 sec. / Number of frames: 20 / Unit: 1/A /
MinMax
Q0.0169 0.2994
Distance distribution function P(R)
Sofotware P(R): GNOM 4.5a / Number of points: 377 /
MinMax
Q0.01785 0.3616
P(R) point1 377
R0 93.68
Result
Type of curve: merged
Comments: Guinier Rg and I(0) were calculated using AutoRg. The experimental MW was estimated using SAXSMOW.
ExperimentalStandardPorod
MW24.1 kDa25.2 kDa-
Volume--22.5 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I0385 0.9681 384.29 1.1
Radius of gyration, Rg2.787 nm0.007 2.71 nm0.063

MinMax
D-9.37
Guinier point5 31

+
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