[English] 日本語
Yorodumi
- PDB-1dfw: CONFORMATIONAL MAPPING OF THE N-TERMINAL SEGMENT OF SURFACTANT PR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dfw
TitleCONFORMATIONAL MAPPING OF THE N-TERMINAL SEGMENT OF SURFACTANT PROTEIN B IN LIPID USING 13C-ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY (FTIR)
ComponentsLUNG SURFACTANT PROTEIN B
KeywordsIMMUNE SYSTEM / LUNG SURFACTANT PROTEIN / SAPOSIN
Function / homology
Function and homology information


Defective pro-SFTPB causes SMDP1 and RDS / multivesicular body lumen / lamellar body / alveolar lamellar body / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / clathrin-coated endocytic vesicle / sphingolipid metabolic process / respiratory gaseous exchange by respiratory system / Surfactant metabolism ...Defective pro-SFTPB causes SMDP1 and RDS / multivesicular body lumen / lamellar body / alveolar lamellar body / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / clathrin-coated endocytic vesicle / sphingolipid metabolic process / respiratory gaseous exchange by respiratory system / Surfactant metabolism / multivesicular body / animal organ morphogenesis / lysosome / endoplasmic reticulum membrane / extracellular region
Similarity search - Function
Saposin A-type domain / Saposin / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains ...Saposin A-type domain / Saposin / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile.
Similarity search - Domain/homology
Pulmonary surfactant-associated protein B
Similarity search - Component
MethodINFRARED SPECTROSCOPY / molecular dynamics, simulated annealing
AuthorsGordon, L.M. / Lee, K.Y.C. / Lipp, M.M. / Zasadzinski, J.A. / Walther, F.J. / Sherman, M.A. / Waring, A.J.
CitationJournal: J.Pept.Res. / Year: 2000
Title: Conformational mapping of the N-terminal segment of surfactant protein B in lipid using 13C-enhanced Fourier transform infrared spectroscopy.
Authors: Gordon, L.M. / Lee, K.Y. / Lipp, M.M. / Zasadzinski, J.A. / Walther, F.J. / Sherman, M.A. / Waring, A.J.
History
DepositionNov 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LUNG SURFACTANT PROTEIN B


Theoretical massNumber of molelcules
Total (without water)2,9331
Polymers2,9331
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)10 / 15structures with acceptable covalent geometry
RepresentativeModel #8closest to the average

-
Components

#1: Protein/peptide LUNG SURFACTANT PROTEIN B


Mass: 2932.701 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-25 / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OCCURS NATURALLY IN HUMANS (HOMO SAPIENS)
References: UniProt: P07988

-
Experimental details

-
Experiment

ExperimentMethod: INFRARED SPECTROSCOPY
NMR experimentType: 13-C isotope enhanced FTIR
NMR detailsText: 13-C isotope enhanced FTIR study. The coordinates in this entry were generated from 13-C induced spectral shifts which give residue-specific secondary structure information.

-
Sample preparation

CrystalDescription: THIS STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES ...Description: THIS STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES 1,3,5,8,10,11,13,14,15,16,18,25. SOLVENT SYSTEM: LIPOSOMES OF 1-PALMITOYL-2-OLEOYL PHOSPHATIDYLGLYCEROL (POPG). SAMPLE CONDITIONS: 298 K, 1 ATM, PH 7.4, IONIC STRENGTH 10 MM PHOSPHATE. TOTAL NUMBER OF CONFORMERS CALCULATED: 15; TOTAL NUMBER OF CONFORMERS SUBMITTED: 10; REPRESENTATIVE CONFORMER 8 (CLOSEST TO THE AVERAGE). SPECTROMETER: MATTSON FTIR RESEARCH SERIES. REFINEMENT METHOD: MOLECULAR DYNAMICS, SIMULATED ANNEALING. SOFTWARE: WINFIRST (FTIR CURVE FITTING SOFTWARE), DISCOVER 2.9.7, MOLECULAR SIMULATIONS, INC. (SAN DIEGO, CA).
DetailsContents: This structure was determined using 13-C isotope enhanced FTIR spectroscopy on a family of selectively labeled chemically synthesized peptides. 13-C carbonyl labels included residues ...Contents: This structure was determined using 13-C isotope enhanced FTIR spectroscopy on a family of selectively labeled chemically synthesized peptides. 13-C carbonyl labels included residues 1,3,5,8,10,11,13,14,15,16,18,25.
Solvent system: Liposomes of 1-palmitoyl-2-oleoyl phosphatidylglycerol (POPG)
Sample conditionsIonic strength: 10 mM phosphate / pH: 7.4 / Pressure: 1 atm / Temperature: 298
Crystal grow
*PLUS
Method: other / Details: FTIR

-
Data collection

NMR spectrometerType: Mattson FTIR Research Series / Manufacturer: Mattson FTIR / Model: Research Series

-
Processing

NMR software
NameVersionDeveloperClassification
Winfirst(FTIR curve fitting software)Kauppine et al.data analysis
Discover2.9.7Molecular Simulations, Inc. (San Diego, CA)refinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
Details: Molecular dynamics (simulated annealing) was used to generate an ensemble of conformers consistent with the FTIR data.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 15 / Conformers submitted total number: 10

+
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