[English] 日本語
Yorodumi
- PDB-3zpm: Solution structure of latherin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zpm
TitleSolution structure of latherin
ComponentsLATHERIN
KeywordsSURFACTANT PROTEIN / PLUNC / BPI
Function / homology
Function and homology information


surfactant homeostasis => GO:0043129 / temperature homeostasis / lipid binding / extracellular region
Similarity search - Function
Latherin / Bactericidal permeability-increasing protein; domain 1 / Lipid-binding serum glycoprotein, N-terminal / Bactericidal permeability-increasing protein, alpha/beta domain superfamily / LBP / BPI / CETP family, N-terminal domain / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesEQUUS CABALLUS (horse)
MethodSOLUTION NMR / AS PER PUBLICATION
AuthorsVance, S.J. / MacDonald, R.E. / Cooper, A. / Kennedy, M.W. / Smith, B.O.
Citation
Journal: J R Soc Interface / Year: 2013
Title: The structure of latherin, a surfactant allergen protein from horse sweat and saliva.
Authors: Vance, S.J. / McDonald, R.E. / Cooper, A. / Smith, B.O. / Kennedy, M.W.
#1: Journal: Plos One / Year: 2009
Title: Latherin: A Surfactant Protein of Horse Sweat and Saliva.
Authors: McDonald, R.E. / Fleming, R.I. / Beeley, J.G. / Bovell, D.L. / Lu, J.R. / Zhao, X. / Cooper, A. / Kennedy, M.W.
#2: Journal: Ph D Thesis / Year: 2012
Title: The Relationship between Structure and Function in Natural Surfactant Proteins
Authors: Vance, S.J.
History
DepositionFeb 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 2.0May 2, 2018Group: Atomic model / Data collection / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 2.1Jun 14, 2023Group: Data collection / Database references / Other
Category: citation / database_2 ...citation / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LATHERIN


Theoretical massNumber of molelcules
Total (without water)22,9101
Polymers22,9101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LEAST RESTRAINT VIOLATION
Representative

-
Components

#1: Protein LATHERIN / DANDER ALLERGEN EQU C 4/EQU C 5 / EQU C 4


Mass: 22910.354 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EQUUS CABALLUS (horse) / Plasmid: PET-32 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P82615

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-HSQC
121CBCA(CO)NH
131CC(CO)NH
141HN(CA)CB
151HN(CA)CO
161HNCO
171HBHA(CO)NH
181HBHANH
191(H)CC(CO)NH
1101BMX C NOESY
1111C HSQC B
1121CH3 TOCSY
1131H(CCO)NH B MX N NOESY
1141CHCH3 TOCSY
1151H(CCO)NH
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED LATHERIN.

-
Sample preparation

DetailsContents: 95% H2O/5% D2O
Sample conditionsIonic strength: 0.07 / pH: 7.5 / Pressure: 1.0 atm / Temperature: 310.0 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
CcpNmr Analysis2.1structure solution
CcpNmr Analysis2.2structure solution
CcpNmr Analysis2structure solution
DANGLE1.1structure solution
TopSpin1.3structure solution
CNS1.2structure solution
RefinementMethod: AS PER PUBLICATION / Software ordinal: 1
Details: REFINEMENT USING NOE, H-BOND AND RDC RESTRAINTS USING ARIA2 AND CNS. DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / 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