[English] 日本語
Yorodumi
- PDB-7s4l: CryoEM structure of Methylotuvimicrobium alcaliphilum 20Z pMMO in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s4l
TitleCryoEM structure of Methylotuvimicrobium alcaliphilum 20Z pMMO in a POPC nanodisc at 2.46 Angstrom resolution
Components(Particulate methane monooxygenase, ...Methane monooxygenase (particulate)) x 3
KeywordsOXIDOREDUCTASE / Complex
Function / homology
Function and homology information


methane monooxygenase (soluble) / methane monooxygenase NADH activity / methane monooxygenase NADPH activity / membrane
Similarity search - Function
Ammonia monooxygenase/particulate methane monooxygenase, subunit A / Ammonia monooxygenase/particulate methane monooxygenase, subunit C / Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily / Ammonia/methane monooxygenase, subunit B, C-terminal / Ammonia monooxygenase/particulate methane monooxygenase, subunit C domain superfamily / Ammonia/particulate methane monooxygenase, subunit A superfamily / Ammonia monooxygenase / Ammonia monooxygenase/methane monooxygenase, subunit C / Ammonia monooxygenase/particulate methane monooxygenase, subunit B / Ammonia/methane monooxygenase, subunitB, N-terminal / Monooxygenase subunit B protein
Similarity search - Domain/homology
Chem-6ER / COPPER (II) ION / DECANE / 1,2-dihexanoyl-sn-glycero-3-phosphocholine / Particulate methane monooxygenase, C subunit / Particulate methane monooxygenase, A subunit / Particulate methane monooxygenase, B subunit
Similarity search - Component
Biological speciesMethylomicrobium alcaliphilum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.46 Å
AuthorsKoo, C.W. / Rosenzweig, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Science / Year: 2022
Title: Recovery of particulate methane monooxygenase structure and activity in a lipid bilayer.
Authors: Christopher W Koo / Frank J Tucci / Yuan He / Amy C Rosenzweig /
Abstract: Bacterial methane oxidation using the enzyme particulate methane monooxygenase (pMMO) contributes to the removal of environmental methane, a potent greenhouse gas. Crystal structures determined using ...Bacterial methane oxidation using the enzyme particulate methane monooxygenase (pMMO) contributes to the removal of environmental methane, a potent greenhouse gas. Crystal structures determined using inactive, detergent-solubilized pMMO lack several conserved regions neighboring the proposed active site. We show that reconstituting pMMO in nanodiscs with lipids extracted from the native organism restores methane oxidation activity. Multiple nanodisc-embedded pMMO structures determined by cryo-electron microscopy to 2.14- to 2.46-angstrom resolution reveal the structure of pMMO in a lipid environment. The resulting model includes stabilizing lipids, regions of the PmoA and PmoC subunits not observed in prior structures, and a previously undetected copper-binding site in the PmoC subunit with an adjacent hydrophobic cavity. These structures provide a revised framework for understanding and engineering pMMO function.
History
DepositionSep 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Particulate methane monooxygenase, B subunit
B: Particulate methane monooxygenase, A subunit
C: Particulate methane monooxygenase, C subunit
H: Particulate methane monooxygenase, C subunit
I: Particulate methane monooxygenase, C subunit
F: Particulate methane monooxygenase, A subunit
G: Particulate methane monooxygenase, A subunit
D: Particulate methane monooxygenase, B subunit
E: Particulate methane monooxygenase, B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,29145
Polymers308,2579
Non-polymers10,03436
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Particulate methane monooxygenase, ... , 3 types, 9 molecules ADEBFGCHI

#1: Protein Particulate methane monooxygenase, B subunit / Methane monooxygenase (particulate)


Mass: 45602.125 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methylomicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z) (bacteria)
Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z
References: UniProt: G4SZ64, methane monooxygenase (soluble)
#2: Protein Particulate methane monooxygenase, A subunit / Methane monooxygenase (particulate)


Mass: 28277.934 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methylomicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z) (bacteria)
Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z
References: UniProt: G4SZ63, methane monooxygenase (soluble)
#3: Protein Particulate methane monooxygenase, C subunit / Methane monooxygenase (particulate)


Mass: 28872.328 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methylomicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z) (bacteria)
Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z
References: UniProt: G4SZ62, methane monooxygenase (soluble)

-
Non-polymers , 5 types, 39 molecules

#4: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu
#5: Chemical
ChemComp-HXG / 1,2-dihexanoyl-sn-glycero-3-phosphocholine / (4R,7R)-7-(hexanoyloxy)-4-hydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphapentadecan-1-aminium 4-oxide


Mass: 454.515 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C20H41NO8P
#6: Chemical
ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H22
#7: Chemical ChemComp-6ER / (S)-2,3-bis(hexanoyloxy)propyl(2-(trimethylammonio)ethyl)phosphate


Mass: 454.515 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H41NO8P
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: pMMO complex in a POPC nanodisc / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Methylotuvimicrobium alcaliphilum 20Z (bacteria)
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 443800 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00721492
ELECTRON MICROSCOPYf_angle_d0.70929310
ELECTRON MICROSCOPYf_dihedral_angle_d22.9892910
ELECTRON MICROSCOPYf_chiral_restr0.0473144
ELECTRON MICROSCOPYf_plane_restr0.0043612

+
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://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