[English] 日本語
Yorodumi
- PDB-1qnd: STEROL CARRIER PROTEIN-2, NMR, 20 STRUCTURES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qnd
TitleSTEROL CARRIER PROTEIN-2, NMR, 20 STRUCTURES
ComponentsNONSPECIFIC LIPID-TRANSFER PROTEIN
KeywordsTRANSFER PROTEIN / STEROL CARRIER PROTEIN 2 / PROTEIN STRUCTURE / PROTEIN DYNAMICS / NITROXIDE SPIN LABELS / LIPID BINDING
Function / homology
Function and homology information


positive regulation of intracellular cholesterol transport / positive regulation of steroid metabolic process / lipid hydroperoxide transport / propanoyl-CoA C-acyltransferase activity / propionyl-CoA C2-trimethyltridecanoyltransferase activity / acetyl-CoA C-myristoyltransferase / progesterone biosynthetic process / acetyl-CoA C-myristoyltransferase activity / Beta-oxidation of pristanoyl-CoA / TYSND1 cleaves peroxisomal proteins ...positive regulation of intracellular cholesterol transport / positive regulation of steroid metabolic process / lipid hydroperoxide transport / propanoyl-CoA C-acyltransferase activity / propionyl-CoA C2-trimethyltridecanoyltransferase activity / acetyl-CoA C-myristoyltransferase / progesterone biosynthetic process / acetyl-CoA C-myristoyltransferase activity / Beta-oxidation of pristanoyl-CoA / TYSND1 cleaves peroxisomal proteins / phosphatidylcholine transfer activity / propanoyl-CoA C-acyltransferase / long-chain fatty acyl-CoA binding / inositol trisphosphate biosynthetic process / phosphatidylinositol transfer activity / fatty acid beta-oxidation using acyl-CoA oxidase / alpha-linolenic acid metabolic process / alpha-linolenic acid (ALA) metabolism / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / regulation of phospholipid biosynthetic process / intracellular cholesterol transport / fatty-acyl-CoA binding / oleic acid binding / bile acid biosynthetic process / phospholipid transport / steroid biosynthetic process / cholesterol transfer activity / bile acid metabolic process / cholesterol binding / fatty acid beta-oxidation / peroxisomal matrix / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / protein localization to plasma membrane / Peroxisomal protein import / peroxisome / signaling receptor binding / endoplasmic reticulum / protein-containing complex / mitochondrion / nucleoplasm / membrane / cytoplasm / cytosol
Similarity search - Function
SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal ...SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Sterol carrier protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLopez-Garcia, F. / Szyperski, T. / Dyer, J.H. / Choinowski, T. / Seedorf, U. / Hauser, H. / Wuthrich, K.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: NMR Structure of the Sterol Carrier Protein-2: Implications for the Biological Role
Authors: Lopez-Garcia, F. / Szyperski, T. / Dyer, J.H. / Choinowski, T. / Seedorf, U. / Hauser, H. / Wuthrich, K.
#1: Journal: FEBS Lett. / Year: 1993
Title: NMR Determination of the Secondary Structure and Three-Dimensional Polypeptide Backbone Fold of the Human Sterol Carrier Protein 2
Authors: Szyperski, T. / Scheek, S. / Johansson, J. / Assmann, G. / Seedorf, U. / Wuthrich, K.
History
DepositionOct 14, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2000Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Atomic model / Version format compliance
Revision 1.2May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NONSPECIFIC LIPID-TRANSFER PROTEIN


Theoretical massNumber of molelcules
Total (without water)13,2601
Polymers13,2601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1

-
Components

#1: Protein NONSPECIFIC LIPID-TRANSFER PROTEIN / SCP-2 / NSL-TP / STEROL CARRIER PROTEIN 2


Mass: 13260.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: CYTOPLASMIC / Organ: LIVER / Plasmid: PGEX-2T/HSCP2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL-1 BLUE / References: UniProt: P22307
Compound detailsDEPOSITED COORDINATES ARE THOSE OF CONFORMERS 1 - 20 IN THE PAPER CITED ON *JRNL* RECORDS ABOVE. NO ...DEPOSITED COORDINATES ARE THOSE OF CONFORMERS 1 - 20 IN THE PAPER CITED ON *JRNL* RECORDS ABOVE. NO VIOLATIONS OF DISTANCE CONSTRAINTS FROM NOES EXCEED 0.11 ANGSTROMS, AND NO VIOLATIONS OF ANGLE CONSTRAINTS EXCEED 4.5 DEGREES.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE PAPER
NMR detailsText: THREE-DIMENSIONAL STRUCTURE IN AQUEOUS SOLUTION REPRESENTED BY 20 CONFORMERS DETERMINED BY NUCLEAR MAGNETIC RESONANCE, TORSION ANGLE DYNAMICS AND RESTRAINED ENERGY REFINEMENT. DATA WERE ...Text: THREE-DIMENSIONAL STRUCTURE IN AQUEOUS SOLUTION REPRESENTED BY 20 CONFORMERS DETERMINED BY NUCLEAR MAGNETIC RESONANCE, TORSION ANGLE DYNAMICS AND RESTRAINED ENERGY REFINEMENT. DATA WERE COLLECTED AT 28 DEGREES CELSIUS AND AT PH 6.0. THEY CONSIST OF 1005 UPPER LIMITS ON DISTANCES OBTAINED FROM NOE MEASUREMENTS AND 584 ANGLE CONSTRAINTS OBTAINED FROM NOE MEASUREMENTS AND COUPLING CONSTANT MEASUREMENTS. THESE INPUT DATA ARE ALSO AVAILABLE FROM THE PROTEIN DATA BANK. SEE JNRK ARTICLE FOR DETAILS

-
Sample preparation

DetailsContents: WATER
Sample conditionsIonic strength: SEE PAPER / pH: 6 / Pressure: AMBIENT / Temperature: 301 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 750 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
OPAL2.6LUGINBUHL, GUNTERT, BILLETER, WUTHRICH STRUCTURAL STATISTICS: ATOMIC RMS DIFFERENCES BACKBONE(N, CA, C', RESIDUES 8-116) 1.00 A BACKBONE(N, CA, C', RESIDUES 8-84) 0.47 A BACKBONE(N, CA, C', RESIDUES 85-116) 1.41 Arefinement
DYANAstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL ARTICLE. TORSION ANGLE DYNAMICS CALCULATIONS WERE PERFORMED WITH THE PROGRAM DYANA (P.GUNTERT, C.MUMENTHALER, K.WUTHRICH, J.MOL.BIOL. (1997) VOL. ...Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL ARTICLE. TORSION ANGLE DYNAMICS CALCULATIONS WERE PERFORMED WITH THE PROGRAM DYANA (P.GUNTERT, C.MUMENTHALER, K.WUTHRICH, J.MOL.BIOL. (1997) VOL. 273, 283-298 FOR THE RESTRAINED ENERGY REFINEMENT. THE PROGRAM OPAL (P. LUGINBHUL, P. GUNTERT, M. BILLETER, K. WUTHRICH J. BIOMOL. NMR (1996), VOL.8, 136-146) WAS USED. THE AVERAGE OF THE RMSD VALUES IN A PAIRWISE COMPARISON OF THE 20 NMR CONFORMERS TO THE MEAN STRUCTURE AS DESCRIBED IN THE PAPER CITED ON *JRNL* RECORDS ABOVE IS 1.0 ANGSTROM FOR THE BACKBONE ATOMS OF RESIDUES 8- 116. THE AVERAGE OF THE RMSD VALUES IN A PAIRWISE COMPARISON TO THE MEAN STRUCTURE FOR RESIDUES 8-84, THUS INCLUDING THE BEST DEFINED FRAGMENT, IS 0.47 ANGSTROMS. THE AVERAGE OF THE RMSD VALUES IN A PAIRWISE COMPARISON TO THE MEAN STRUCTURE FOR RESIDUES 85-116, THUS INCLUDING THE WORSE DEFINED RESIDUES IS 1.41 ANGSTROMS.
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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://pdbjlvh1.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