[English] 日本語
Yorodumi
- PDB-7ojg: CRYO-EM STRUCTURE OF UNDECAMERIC SLYB FROM ESCHERICHIA COLI K12 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ojg
TitleCRYO-EM STRUCTURE OF UNDECAMERIC SLYB FROM ESCHERICHIA COLI K12
ComponentsOuter membrane lipoprotein slyB
KeywordsMEMBRANE PROTEIN / OUTER MEMBRANE CHAPERONE / 2TM GLYCINE ZIPPER / OUTER MEMBRANE LIPOPROTEIN SLYB / LPS-LP BINDING PROTEIN
Function / homology: / Glycine zipper 2TM domain / Glycine zipper 2TM domain / outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Chem-L8Z / Chem-LPP / PALMITIC ACID / Outer membrane lipoprotein slyB
Function and homology information
Biological speciesEscherichia coli BW25113 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsNguyen, V.S. / Remaut, H.
Funding support Belgium, 4items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0G0818N Belgium
Research Foundation - Flanders (FWO)G0H5916N Belgium
Research Foundation - Flanders (FWO)FWOTM903 Belgium
Research Foundation - Flanders (FWO)12ZM421N Belgium
CitationJournal: Nature / Year: 2023
Title: SlyB encapsulates outer membrane proteins in stress-induced lipid nanodomains
Authors: Janssens, A. / Nguyen, V.S. / Cecil, A.J. / Van der Verren, S.E. / Timmerman, E. / Deghelt, M. / Pak, A.J. / Collet, J.F. / Impens, F. / Remaut, H.
History
DepositionMay 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer membrane lipoprotein slyB
B: Outer membrane lipoprotein slyB
C: Outer membrane lipoprotein slyB
D: Outer membrane lipoprotein slyB
E: Outer membrane lipoprotein slyB
F: Outer membrane lipoprotein slyB
G: Outer membrane lipoprotein slyB
H: Outer membrane lipoprotein slyB
I: Outer membrane lipoprotein slyB
J: Outer membrane lipoprotein slyB
K: Outer membrane lipoprotein slyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,47877
Polymers171,75011
Non-polymers38,72866
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "A"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1chain "K"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1CYSARGC1 - 138
d_12ens_1PLMPLMC
d_13ens_1GOLGOLC
d_14ens_1PLMPLMC
d_15ens_1PLMPLMC
d_16ens_1PA1PA1C
d_17ens_1GCSGCSC
d_18ens_1KDOKDOC
d_19ens_1FTTFTTC
d_110ens_1FTTFTTC
d_111ens_1FTTFTTC
d_112ens_1DAODAOC
d_113ens_1FTTFTTC
d_114ens_1MYRMYRC
d_115ens_1PO4PO4C
d_116ens_1PO4PO4C
d_117ens_1PEFPEFC
d_21ens_1CYSARGB1 - 138
d_22ens_1PLMPLMB
d_23ens_1GOLGOLB
d_24ens_1PLMPLMB
d_25ens_1PLMPLMB
d_26ens_1PA1PA1B
d_27ens_1GCSGCSB
d_28ens_1KDOKDOB
d_29ens_1FTTFTTB
d_210ens_1FTTFTTB
d_211ens_1FTTFTTB
d_212ens_1DAODAOB
d_213ens_1FTTFTTB
d_214ens_1MYRMYRB
d_215ens_1PO4PO4B
d_216ens_1PO4PO4B
d_217ens_1PEFPEFB
d_31ens_1CYSARGA1 - 138
d_32ens_1PLMPLMA
d_33ens_1GOLGOLA
d_34ens_1PLMPLMA
d_35ens_1PLMPLMA
d_36ens_1PA1PA1A
d_37ens_1GCSGCSA
d_38ens_1KDOKDOA
d_39ens_1FTTFTTA
d_310ens_1FTTFTTA
d_311ens_1FTTFTTA
d_312ens_1DAODAOA
d_313ens_1FTTFTTA
d_314ens_1MYRMYRA
d_315ens_1PO4PO4A
d_316ens_1PO4PO4A
d_317ens_1PEFPEFA
d_41ens_1CYSARGD1 - 138
d_42ens_1PLMPLMD
d_43ens_1GOLGOLD
d_44ens_1PLMPLMD
d_45ens_1PLMPLMD
d_46ens_1PA1PA1D
d_47ens_1GCSGCSD
d_48ens_1KDOKDOD
d_49ens_1FTTFTTD
d_410ens_1FTTFTTD
d_411ens_1FTTFTTD
d_412ens_1DAODAOD
d_413ens_1FTTFTTD
d_414ens_1MYRMYRD
d_415ens_1PO4PO4D
d_416ens_1PO4PO4D
d_417ens_1PEFPEFD
d_51ens_1CYSARGE1 - 138
d_52ens_1PLMPLME
d_53ens_1GOLGOLE
d_54ens_1PLMPLME
d_55ens_1PLMPLME
d_56ens_1PA1PA1E
d_57ens_1GCSGCSE
d_58ens_1KDOKDOE
d_59ens_1FTTFTTE
d_510ens_1FTTFTTE
d_511ens_1FTTFTTE
d_512ens_1DAODAOE
d_513ens_1FTTFTTE
d_514ens_1MYRMYRE
d_515ens_1PO4PO4E
d_516ens_1PO4PO4E
d_517ens_1PEFPEFE
d_61ens_1CYSARGF1 - 138
d_62ens_1PLMPLMF
d_63ens_1GOLGOLF
d_64ens_1PLMPLMF
d_65ens_1PLMPLMF
d_66ens_1PA1PA1F
d_67ens_1GCSGCSF
d_68ens_1KDOKDOF
d_69ens_1FTTFTTF
d_610ens_1FTTFTTF
d_611ens_1FTTFTTF
d_612ens_1DAODAOF
d_613ens_1FTTFTTF
d_614ens_1MYRMYRF
d_615ens_1PO4PO4F
d_616ens_1PO4PO4F
d_617ens_1PEFPEFF
d_71ens_1CYSARGG1 - 138
d_72ens_1PLMPLMG
d_73ens_1GOLGOLG
d_74ens_1PLMPLMG
d_75ens_1PLMPLMG
d_76ens_1PA1PA1G
d_77ens_1GCSGCSG
d_78ens_1KDOKDOG
d_79ens_1FTTFTTG
d_710ens_1FTTFTTG
d_711ens_1FTTFTTG
d_712ens_1DAODAOG
d_713ens_1FTTFTTG
d_714ens_1MYRMYRG
d_715ens_1PO4PO4G
d_716ens_1PO4PO4G
d_717ens_1PEFPEFG
d_81ens_1CYSARGH1 - 138
d_82ens_1PLMPLMH
d_83ens_1GOLGOLH
d_84ens_1PLMPLMH
d_85ens_1PLMPLMH
d_86ens_1PA1PA1H
d_87ens_1GCSGCSH
d_88ens_1KDOKDOH
d_89ens_1FTTFTTH
d_810ens_1FTTFTTH
d_811ens_1FTTFTTH
d_812ens_1DAODAOH
d_813ens_1FTTFTTH
d_814ens_1MYRMYRH
d_815ens_1PO4PO4H
d_816ens_1PO4PO4H
d_817ens_1PEFPEFH
d_91ens_1CYSARGI1 - 138
d_92ens_1PLMPLMI
d_93ens_1GOLGOLI
d_94ens_1PLMPLMI
d_95ens_1PLMPLMI
d_96ens_1PA1PA1I
d_97ens_1GCSGCSI
d_98ens_1KDOKDOI
d_99ens_1FTTFTTI
d_910ens_1FTTFTTI
d_911ens_1FTTFTTI
d_912ens_1DAODAOI
d_913ens_1FTTFTTI
d_914ens_1MYRMYRI
d_915ens_1PO4PO4I
d_916ens_1PO4PO4I
d_917ens_1PEFPEFI
d_101ens_1CYSARGJ1 - 138
d_102ens_1PLMPLMJ
d_103ens_1GOLGOLJ
d_104ens_1PLMPLMJ
d_105ens_1PLMPLMJ
d_106ens_1PA1PA1J
d_107ens_1GCSGCSJ
d_108ens_1KDOKDOJ
d_109ens_1FTTFTTJ
d_1010ens_1FTTFTTJ
d_1011ens_1FTTFTTJ
d_1012ens_1DAODAOJ
d_1013ens_1FTTFTTJ
d_1014ens_1MYRMYRJ
d_1015ens_1PO4PO4J
d_1016ens_1PO4PO4J
d_1017ens_1PEFPEFJ
d_111ens_1CYSARGK1 - 138
d_112ens_1PLMPLMK
d_113ens_1GOLGOLK
d_114ens_1PLMPLMK
d_115ens_1PLMPLMK
d_116ens_1PA1PA1K
d_117ens_1GCSGCSK
d_118ens_1KDOKDOK
d_119ens_1FTTFTTK
d_1110ens_1FTTFTTK
d_1111ens_1FTTFTTK
d_1112ens_1DAODAOK
d_1113ens_1FTTFTTK
d_1114ens_1MYRMYRK
d_1115ens_1PO4PO4K
d_1116ens_1PO4PO4K
d_1117ens_1PEFPEFK

-
Components

#1: Protein
Outer membrane lipoprotein slyB


Mass: 15613.606 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Strain: 2002017 / Gene: slyB, SFxv_1871 / Production host: Escherichia coli (E. coli) / References: UniProt: D2AGE2
#2: Chemical...
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-L8Z / (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(~{E},3~{R})-3-dodecanoyloxytetradec-5-enoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(~{E},3~{R})-3-oxidanyltetradec-11-enoyl]amino]-4-[(~{E},3~{R})-3-oxidanyltetradec-5-enoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(~{E},3~{R})-3-tetradecanoyloxytetradec-7-enoyl]oxy-oxan-2-yl]methoxy]-4,5-bis(oxidanyl)oxane-2-carboxylic acid


Mass: 2010.478 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C102H182N2O32P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C35H69O8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Outer membrane lipoprotein SlyB / Type: COMPLEX
Details: Undecameric SlyB was purified from overexpression of SlyB-TEV-HIS in E. coli using using 2-step Ni-IMAC purification.
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.20 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli BW25113 (bacteria) / Cellular location: Outer membrane
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pASK-IBA
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mMtris(hydroxymethyl)aminomethaneTris1
30.03 %N-Dodecyl-beta-MaltosideDDM1
SpecimenConc.: 0.04 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Details: Back-blotting for 4 seconds before plunging

-
Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm / Cs: 2.55 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 3 sec. / Electron dose: 61 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6352

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameVersionCategoryDetails
1crYOLO1.7particle selectionusing a trained model
2SerialEM3.8.2image acquisition
4RELION3.1CTF correctionParticle extraction, 3D classification, and 3D reconstruction
5CTFFIND4CTF correctionCTF estimation
6MotionCorr21.3CTF correctionMotion correction
7PHENIXCTF correctionRefinement, Auto_sharpen, geometry optimisation
8Coot0.8.9CTF correctionModel building and editing
9UCSF Chimera1.15CTF correctionMap manipulation and display
10PyMOL2.2CTF correctionDisplay
11SerialEMCTF correctionImage acquisition
14Cootmodel fitting
16PHENIXmodel refinementusing phenix.real_space_refine
19RELION3.1classification
20RELION3.13D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C11 (11 fold cyclic)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145472 / Symmetry type: POINT
Atomic model buildingB value: 35 / Protocol: AB INITIO MODEL / Space: REAL
RefinementHighest resolution: 3.4 Å
Displacement parametersBiso mean: 67.35 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005513310
ELECTRON MICROSCOPYf_angle_d0.90217567
ELECTRON MICROSCOPYf_chiral_restr0.05161925
ELECTRON MICROSCOPYf_plane_restr0.00452112
ELECTRON MICROSCOPYf_dihedral_angle_d13.74943014
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BELECTRON MICROSCOPYNCS constraints0.000703917175021
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.000696495008482
ens_1d_4DELECTRON MICROSCOPYNCS constraints0.000711661665346
ens_1d_5EELECTRON MICROSCOPYNCS constraints0.000712126139912
ens_1d_6FELECTRON MICROSCOPYNCS constraints0.000703715699321
ens_1d_7GELECTRON MICROSCOPYNCS constraints0.000710836961203
ens_1d_8HELECTRON MICROSCOPYNCS constraints0.000713851392781
ens_1d_9IELECTRON MICROSCOPYNCS constraints0.000719233127718
ens_1d_10JELECTRON MICROSCOPYNCS constraints0.000710845295032
ens_1d_11KELECTRON MICROSCOPYNCS constraints0.000709802556083

+
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