[English] 日本語
Yorodumi
- PDB-2lsh: Solution structure of the class I hydrophobin DewA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lsh
TitleSolution structure of the class I hydrophobin DewA
ComponentsSpore-wall fungal hydrophobin dewA
KeywordsPROTEIN FIBRIL / hydrophobin / functional amyloid / surface active protein
Function / homology
Function and homology information


asexual spore wall assembly / spore wall / structural constituent of cell wall / fungal-type cell wall / extracellular region
Similarity search - Function
Fungal hydrophobin / Hydrophobin, conserved site / Fungal hydrophobins signature. / Hydrophobin / Hydrophobins
Similarity search - Domain/homology
Spore-wall fungal hydrophobin dewA
Similarity search - Component
Biological speciesAspergillus nidulans (mold)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsclosest to the average, model1
AuthorsMorris, V.K. / Kwan, A.H. / Mackay, J.P. / Sunde, M.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Analysis of the structure and conformational states of DewA gives insight into the assembly of the fungal hydrophobins
Authors: Morris, V.K. / Kwan, A.H. / Sunde, M.
History
DepositionApr 30, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spore-wall fungal hydrophobin dewA


Theoretical massNumber of molelcules
Total (without water)11,4581
Polymers11,4581
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 / 500structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Spore-wall fungal hydrophobin dewA


Mass: 11457.821 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans (mold) / Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: dewA, AN8006 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52750

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1342D 1H-1H NOESY
1423D CBCA(CO)NH
1523D C(CO)NH
1623D HNCO
1723D HN(CA)CB
1823D HBHA(CO)NH
1923D HN(CA)CO
11013D 1H-15N NOESY
11113D 1H-15N TOCSY
21233D 1H-13C NOESY aliphatic
21333D (H)CCH-TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
1300-500 uM [U-99% 15N] DewA-1, 0.1 mM DSS-2, 20 mM sodium acetate-3, 95 % H20-4, 5 % D20-5, 95% H2O/5% D2O95% H2O/5% D2O
2300-500 uM [U-98% 13C; U-98% 15N] DewA-6, 0.1 mM DSS-7, 20 mM sodium acetate-8, 95 % H20-9, 5 % D20-10, 95% H2O/5% D2O95% H2O/5% D2O
3300-500 uM [U-98% 13C; U-98% 15N] DewA-11, 0.1 mM DSS-12, 20 mM sodium acetate-13, 95 % H20-14, 5 % D20-15, 100% D2O100% D2O
4300-500 uM [U-98% 13C; U-98% 15N] DewA-16, 0.1 mM DSS-17, 20 mM sodium acetate-18, 95 % H20-19, 5 % D20-20, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
uMDewA-1[U-99% 15N]300-5001
0.1 mMDSS-21
20 mMsodium acetate-31
95 %H20-41
5 %D20-51
uMDewA-6[U-98% 13C; U-98% 15N]300-5002
0.1 mMDSS-72
20 mMsodium acetate-82
95 %H20-92
5 %D20-102
uMDewA-11[U-98% 13C; U-98% 15N]300-5003
0.1 mMDSS-123
20 mMsodium acetate-133
95 %H20-143
5 %D20-153
uMDewA-16[U-98% 13C; U-98% 15N]300-5004
0.1 mMDSS-174
20 mMsodium acetate-184
95 %H20-194
5 %D20-204
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
140 5.5 1 atm298 K
240 5.1 1 atm298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIArefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20 / Representative conformer: 8

+
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