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- EMDB-38500: Cryo-EM structure of Deinococcus radiodurans BamA -

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Basic information

Entry
Database: EMDB / ID: EMD-38500
TitleCryo-EM structure of Deinococcus radiodurans BamA
Map data
Sample
  • Complex: dimer of Deinococcus radioduransr BamA
    • Protein or peptide: Outer membrane protein assembly factor BamA
KeywordsMEMBRANE PROTEIN / Outer membrane protein
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Polypeptide-transport-associated, ShlB-type / POTRA domain, ShlB-type / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain
Similarity search - Domain/homology
Outer membrane protein
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsQian HW / Wang ZZ
Funding support China, 1 items
OrganizationGrant numberCountry
Other privateKY9100000034 China
CitationJournal: Justc / Year: 2024
Title: Structural insights into Deinococcus radiodurans BamA: extracellular loop diversity and its evolutionary implications
Authors: Wang ZZ / Xue JC / Wang JJ / Yu JG / Qian HW / Yang XX
History
DepositionDec 29, 2023-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38500.png

Downloads & links

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Map

FileDownload / File: emd_38500.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 180 pix.
= 192.6 Å		1.07 Å/pix.
x 180 pix.
= 192.6 Å		1.07 Å/pix.
x 180 pix.
= 192.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.357
Minimum - Maximum-3.7887247 - 4.602451
Average (Standard dev.)0.009438028 (±0.12310285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 192.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38500_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38500_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : dimer of Deinococcus radioduransr BamA

EntireName: dimer of Deinococcus radioduransr BamA
Components
  • Complex: dimer of Deinococcus radioduransr BamA
    • Protein or peptide: Outer membrane protein assembly factor BamA

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Supramolecule #1: dimer of Deinococcus radioduransr BamA

SupramoleculeName: dimer of Deinococcus radioduransr BamA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)

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Macromolecule #1: Outer membrane protein assembly factor BamA

MacromoleculeName: Outer membrane protein assembly factor BamA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
Strain: ATCC 13939 / R1 / DSM 20539
Molecular weightTheoretical: 93.809844 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKYLLPTAAA GLLLLAAQPA MAGSDYKDDD DKSGHHHHHH HHHHGSDEVD AGSQQAGTVQ DISVVGTTDL LSEFLKTTLT VQPGAALSS VNLRQVEQEV LASGYFKTAT AELRTTGGRD TLVVTVTANP VIKDVQATGL TFLPADAFKQ SVAELLNIAP G AVLNTQRL ...String:
MKYLLPTAAA GLLLLAAQPA MAGSDYKDDD DKSGHHHHHH HHHHGSDEVD AGSQQAGTVQ DISVVGTTDL LSEFLKTTLT VQPGAALSS VNLRQVEQEV LASGYFKTAT AELRTTGGRD TLVVTVTANP VIKDVQATGL TFLPADAFKQ SVAELLNIAP G AVLNTQRL EQAKEALAQN YRQEGFPFVP SISADTKTNK DGTATVTFVV DESAPLSRIE VTGATLLPQA TVQNIFRPLQ TS KRFTTQA FFAASDALQA AYEAAGYFQA GIDPRSVTLE NGVLKLSVIE SRVASVDLSP LGTLAQTPAL QTKAGQPLRL AQL QADVRA LANQTGQPVG FALQADPQNP SQVTVLFGAA DVESGPVKSI AFVGNTKVPT AQLQAAIKTK PGDVYSPQLA QDDF MALRN VYRQAGYEIS TRDAITFQNG VLTYNLREVR LAGYELAWQG QHRTKDRVIL RELPAAGQTF NSKDVQAALG RVSAL GYVT INDVRVKSDP QNPENVTYVI ALSEGRTGIP VNLSLGYDSL QGGWSGDVAY TNSNAFGLGH SFGVRLGAVQ NQAGQN WVG SLNYTIPWLD LDFADFRKNR TSLSFGVGSD VGGNIALLDA NKEDTGRDYT TRTNGFSLGL GRNITPNLTA SANVAFN NR TSYLEPKQEG ETSNLDDAAA TALLPATSLT TRLSGNLNYD NTDNVNFPGR GVRAYGALGY NVGRAGDAPL SWTDGEIG V SGYYGFGGRI KRSFGLETYR QVLAARANTG TTTGTFPDGT GYFIGGSNPL ASRELRGLED GQLFGTNYFS SSLEYRYDF GLSGGVAQGL YGVLFADYGG VWNSGEAFRS AYGVGAGVQL NLGFGGAQLP SLRFDYGYSG QNAQKPNGRF HFRIGNFW

UniProtKB: Outer membrane protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 607784
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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