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- PDB-7ojg: CRYO-EM STRUCTURE OF UNDECAMERIC SLYB FROM ESCHERICHIA COLI K12 -

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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 / homologyGlycine zipper 2TM domain / Glycine zipper 2TM domain / cell 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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

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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 / 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 / Glycerol


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

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Experimental details

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Experiment

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

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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 chlorideNaClSodium chloride1
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

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / 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

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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

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