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- EMDB-21901: CryoEM structure of Burkholderia pseudomallei hopanoid biosynthes... -

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Basic information

Entry
Database: EMDB / ID: EMD-21901
TitleCryoEM structure of Burkholderia pseudomallei hopanoid biosynthesis-associated RND transporter HpnN
Map datadensity modification in Phenix
Sample
  • Complex: hopanoid transporter HpnN
    • Protein or peptide: Hopanoid biosynthesis associated RND transporter like protein HpnN
KeywordsCryoEM structure / hopanoid transporter HpnN / PROTEIN TRANSPORT
Function / homologyHopanoid biosynthesis associated RND transporter-like protein HpnN / Membrane transport protein MMPL domain / MMPL family / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / membrane => GO:0016020 / plasma membrane / Hopanoid biosynthesis associated RND transporter like protein HpnN
Function and homology information
Biological speciesEscherichia Coli (E. coli) / Burkholderia pseudomallei MSHR346 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsLyu M / Yu EW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Methods / Year: 2021
Title: A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins.
Authors: Chih-Chia Su / Meinan Lyu / Christopher E Morgan / Jani Reddy Bolla / Carol V Robinson / Edward W Yu /
Abstract: Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein ...Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein samples hampers the progress of their structural determination. Here, we develop a bottom-up iterative method, Build and Retrieve (BaR), that enables the identification and determination of cryo-EM structures of a variety of inner and outer membrane proteins, including membrane protein complexes of different sizes and dimensions, from a heterogeneous, impure protein sample. We also use the BaR methodology to elucidate structural information from Escherichia coli K12 crude membrane and raw lysate. The findings demonstrate that it is possible to solve high-resolution structures of a number of relatively small (<100 kDa) and less abundant (<10%) unidentified membrane proteins within a single, heterogeneous sample. Importantly, these results highlight the potential of cryo-EM for systems structural proteomics.
History
DepositionMay 4, 2020-
Header (metadata) releaseFeb 3, 2021-
Map releaseFeb 3, 2021-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wu0
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21901.png

Downloads & links

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Map

FileDownload / File: emd_21901.map.gz / Format: CCP4 / Size: 2.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdensity modification in Phenix
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 120 pix.
= 129.6 Å		1.08 Å/pix.
x 69 pix.
= 74.52 Å		1.08 Å/pix.
x 82 pix.
= 88.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-7.667325 - 15.212773
Average (Standard dev.)0.000000000033757 (±0.64826655)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin11710676
Dimensions6982120
Spacing8269120
CellA: 88.560005 Å / B: 74.520004 Å / C: 129.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z8269120
origin x/y/z0.0000.0000.000
length x/y/z88.56074.520129.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS10611776
NC/NR/NS8269120
D min/max/mean-7.66715.2130.000

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Supplemental data

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Additional map: orignal in cryosparc

Fileemd_21901_additional_1.map
Annotationorignal in cryosparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : hopanoid transporter HpnN

EntireName: hopanoid transporter HpnN
Components
  • Complex: hopanoid transporter HpnN
    • Protein or peptide: Hopanoid biosynthesis associated RND transporter like protein HpnN

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Supramolecule #1: hopanoid transporter HpnN

SupramoleculeName: hopanoid transporter HpnN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia Coli (E. coli)

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Macromolecule #1: Hopanoid biosynthesis associated RND transporter like protein HpnN

MacromoleculeName: Hopanoid biosynthesis associated RND transporter like protein HpnN
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Burkholderia pseudomallei MSHR346 (bacteria)
Molecular weightTheoretical: 92.60093 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLTSVLVRLV AWSVRRPIWV VVLSLVIAAL SSVYVAHHFK INTDISKLVE NDPKWAALGR AIDDAFPQRN QTILAVVEAP APEFAGAAA DALAEGLRRE TEAGRIGQVS EPAGGPLFEH DGLLFLPEQD VATTTAQLAS ARPLINVLAK DPSIAGLATT L STTLGVPL ...String:
MLTSVLVRLV AWSVRRPIWV VVLSLVIAAL SSVYVAHHFK INTDISKLVE NDPKWAALGR AIDDAFPQRN QTILAVVEAP APEFAGAAA DALAEGLRRE TEAGRIGQVS EPAGGPLFEH DGLLFLPEQD VATTTAQLAS ARPLINVLAK DPSIAGLATT L STTLGVPL QSGQVKLSGM AKLLSRSAAT VDDVLAGKPA AFSWRALVDA DAAREPARAF VTVQPVVNYG ALKAGEQASR TI RATAQAL KLDERFGAAV RLTGEQPLAD EEFASVQDGA LVNGIATLAI VLVILWIALR SKRMIASVFV TLFVGLVVTA ALG LMMVGS LNMISVAFMV LFVGLGVDFA IQYGVKYREE RHRDPNLDHA LVGAAHAMGM PLTLATAAVA ASFFSFLPTA YRGV SELGL IAGVGMFVAL FTTLTLLPAL LKLLAPPGER KPPGFPRLAP VDDYLDHHRK PILIGTLAVV IGALPLLAHL RFDFN PLHL KDPRSESMAT LLALKDSPEA SVNDVSLLAP SLVAANAAAQ RLGALPEVGR TTTLSTFIPD AQPQKLATIA AAARGL LPA LTQPAAAPVP DAQRVAALKR ASNLLEYASE DYPGPGAAAA KHLSESLAKL AAADAATRER AEHAFSVPLK IALNQLA ML LQPLEITREN LPPQIVRDWI APDGRALVQI SPKVVKGADP GDDAMLRRFA KAVKAAEPGA IGGPISILHS ADTIIRAF L QAAALSVVSI TVLLWITLRR FGDVLRTLVP LLVSGVVTLE LCVLLGMPLN FANIIALPLM LGVGVAFKVY FVMAWRAGQ TGLLQSSLTH AVLFSAATTA TAFGSLWLSH HPGTASMGRL LALALSCTLI GAVVFQPVLM GKPRTKRVTN QSQGIDE

UniProtKB: Hopanoid biosynthesis associated RND transporter like protein HpnN

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63910
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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