[English] 日本語
Yorodumi
- PDB-5ml1: NMR Structure of the Littorina littorea metallothionein, a snail ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ml1
TitleNMR Structure of the Littorina littorea metallothionein, a snail MT folding into three distinct domains
ComponentsPutative metallothionein
KeywordsMETAL BINDING PROTEIN / NMR metallothionein metal cluster metalloprotein
Function / homologyMetallothionein, mollusc / metal ion binding / : / Putative metallothionein
Function and homology information
Biological speciesLittorina littorea (invertebrata)
MethodSOLUTION NMR
AuthorsBaumann, C. / Beil, A. / Jurt, S. / Zerbe, O.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationI 1482-N28 Switzerland
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Structural Adaptation of a Protein to Increased Metal Stress: NMR Structure of a Marine Snail Metallothionein with an Additional Domain.
Authors: Baumann, C. / Beil, A. / Jurt, S. / Niederwanger, M. / Palacios, O. / Capdevila, M. / Atrian, S. / Dallinger, R. / Zerbe, O.
History
DepositionDec 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 19, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative metallothionein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,20710
Polymers10,1961
Non-polymers1,0129
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

-
Components

#1: Protein Putative metallothionein


Mass: 10195.717 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: the first 3 residues (GSM) are artefacts from the Thrombin cleavage or non-processed start codon The first real residue is Ser-4
Source: (gene. exp.) Littorina littorea (invertebrata) / Plasmid: pGEX-4T-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q962G0
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC aliphatic
132isotropic13D CBCA(CO)NH
1132isotropic13D HBHA(CO)NH
142isotropic13D HN(CA)CB
152isotropic13D HNCO
192isotropic13D HN(CA)CO
1102isotropic13D (H)CCH-TOCSY
1113isotropic3113Cd-1H HSQC
1123isotropic3113Cd-HSQC-TOCSY
182isotropic13D 1H-13C NOESY aliphatic
171isotropic13D 1H-15N NOESY

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM [U-99% 15N] Ll-MT, 90% H2O/10% D2O15N-labeled protein, used for 15N-NOESY15N-LlMT (Cd)990% H2O/10% D2O
solution20.5 mM [U-99% 13C; U-99% 15N] Metallothionein from Littorina Littorea, 90% H2O/10% D2O13C,15N uniformly labelled LlMT, used for backbone and sidechain assignment and for 13C-NOESY13C,15N-LlMT (Cd)990% H2O/10% D2O
solution32 mM [U-99% 15N]113Cd Metallothionein from Littorina Littorea, 90% H2O/10% D2O15N-labeled protein, with 113Cd for measurements of 113Cd,1H correlation spectra 10 mM TCEP113 Cd Sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMLl-MT[U-99% 15N]1
0.5 mMMetallothionein from Littorina Littorea[U-99% 13C; U-99% 15N]2
2 mMMetallothionein from Littorina Littorea[U-99% 15N]113Cd3
Sample conditionsDetails: 1.0 mM TMSP 20 mM Tris buffer 1 mM TCEP (except for 113Cd Sample)
Ionic strength: 20 mM / Ionic strength err: 1 / Label: sample_pH7.0 / pH: 7.0 / PH err: 0.05 / Pressure: 1 bar / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE7001with cryo probe
Bruker AVANCEBrukerAVANCE6002with cryo probe
Bruker AVANCE IIBrukerAVANCE II5003with cryo probe

-
Processing

NMR software
NameVersionDeveloperClassification
CARA1.9.0 Beta 7Keller and Wuethrichchemical shift assignment
CcpNmr Analysis2.4 release 2CCPNchemical shift assignment
CYANA3.97Guentert, Mumenthaler and Wuethrichstructure calculation
CNS-XPLORBruenger and Schwietersgeometry optimization
NMR ensembleConformers 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