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- EMDB-35643: Cryo-EM structure of heme transporter CydDC from Escherichia coli... -

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Basic information

Entry
Database: EMDB / ID: EMD-35643
TitleCryo-EM structure of heme transporter CydDC from Escherichia coli in the occluded ATP bound state
Map data
Sample
  • Complex: CydDC
    • Protein or peptide: ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC
    • Protein or peptide: ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsABC transporter / Heme / TRANSPORT PROTEIN
Function / homology
Function and homology information


cysteine transport / glutathione transmembrane transport / ABC-type oligopeptide transporter activity / ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / cell redox homeostasis / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC / ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC / ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC / ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhu C / Li J
Funding support China, 5 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA1300900 China
Ministry of Science and Technology (MoST, China)22ZR1441600 China
Other government22ZR1441600
Other governmentZD2021CY001
Other governmentLG202101-01-08 China
CitationJournal: Protein Cell / Year: 2023
Title: Cryo-EM structures of a prokaryotic heme transporter CydDC.
Authors: Chen Zhu / Yanfeng Shi / Jing Yu / Wenhao Zhao / Lingqiao Li / Jingxi Liang / Xiaolin Yang / Bing Zhang / Yao Zhao / Yan Gao / Xiaobo Chen / Xiuna Yang / Lu Zhang / Luke W Guddat / Lei Liu / ...Authors: Chen Zhu / Yanfeng Shi / Jing Yu / Wenhao Zhao / Lingqiao Li / Jingxi Liang / Xiaolin Yang / Bing Zhang / Yao Zhao / Yan Gao / Xiaobo Chen / Xiuna Yang / Lu Zhang / Luke W Guddat / Lei Liu / Haitao Yang / Zihe Rao / Jun Li /
History
DepositionMar 14, 2023-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35643.png

Downloads & links

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Map

FileDownload / File: emd_35643.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 320 pix.
= 307.2 Å		0.96 Å/pix.
x 320 pix.
= 307.2 Å		0.96 Å/pix.
x 320 pix.
= 307.2 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.90131086 - 1.8307837
Average (Standard dev.)0.0033732967 (±0.056329962)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 307.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35643_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_35643_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 : CydDC

EntireName: CydDC
Components
  • Complex: CydDC
    • Protein or peptide: ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC
    • Protein or peptide: ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: CydDC

SupramoleculeName: CydDC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: ABC transporter, CydDC cysteine exporter (CydDC-E) family, permea...

MacromoleculeName: ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 62.978914 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MRALLPYLAL YKRHKWMLSL GIVLAIVTLL ASIGLLTLSG WFLSASAVAG VAGLYSFNYM LPAAGVRGAA ITRTAGRYFE RLVSHDATF RVLQHLRIYT FSKLLPLSPA GLARYRQGEL LNRVVADVDT LDHLYLRVIS PLVGAFVVIM VVTIGLSFLD F TLAFTLGG ...String:
MRALLPYLAL YKRHKWMLSL GIVLAIVTLL ASIGLLTLSG WFLSASAVAG VAGLYSFNYM LPAAGVRGAA ITRTAGRYFE RLVSHDATF RVLQHLRIYT FSKLLPLSPA GLARYRQGEL LNRVVADVDT LDHLYLRVIS PLVGAFVVIM VVTIGLSFLD F TLAFTLGG IMLLTLFLMP PLFYRAGKST GQNLTHLRGQ YRQQLTAWLQ GQAELTIFGA SDRYRTQLEN TEIQWLEAQR RQ SELTALS QAIMLLIGAL AVILMLWMAS GGVGGNAQPG ALIALFVFCA LAAFEALAPV TGAFQHLGQV IASAVRITDL TDQ KPEVTF PDTQTRVADR VSLTLRDVQF TYPEQSQQAL KGISLQVNAG EHIAILGRTG CGKSTLLQLL TRAWDPQQGE ILLN DSPIA SLNEAALRQT ISVVPQRVHL FSATLRDNLL LASPGSSDEA LSEILRRVGL EKLLEDAGLN SWLGEGGRQL SGGEL RRLA IARALLHDAP LVLLDQPTEG LDATTESQIL ELLAEMMREK TVLMVTHRLR GLSRFQQIIV MDNGQIIEQG THAELL ARQ GRYYQFKQGL

UniProtKB: ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC

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Macromolecule #2: ABC transporter, CydDC cysteine exporter (CydDC-E) family, permea...

MacromoleculeName: ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: B / BL21-DE3
Molecular weightTheoretical: 65.143953 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MNKSRQKELT RWLKQQSVIS QRWLNISRLL GFVSGILIIA QAWFMARILQ HMIMENIPRE ALLLPFTLLV LTFVLRAWVV WLRERVGYH AGQHIRFAIR RQVLDRLQQA GPAWIQGKPA GSWATLVLEQ IDDMHDYYAR YLPQMALAVS VPLLIVVAIF P SNWAAALI ...String:
MNKSRQKELT RWLKQQSVIS QRWLNISRLL GFVSGILIIA QAWFMARILQ HMIMENIPRE ALLLPFTLLV LTFVLRAWVV WLRERVGYH AGQHIRFAIR RQVLDRLQQA GPAWIQGKPA GSWATLVLEQ IDDMHDYYAR YLPQMALAVS VPLLIVVAIF P SNWAAALI LLGTAPLIPL FMALVGMGAA DANRRNFLAL ARLSGHFLDR LRGMETLRIF GRGEAEIESI RSASEDFRQR TM EVLRLAF LSSGILEFFT SLSIALVAVY FGFSYLGELD FGHYDTGVTL AAGFLALILA PEFFQPLRDL GTFYHAKAQA VGA ADSLKT FMETPLAHPQ RGEAELALTD PLTIEAEDLF ITSPEGKTLA GPLNFTLPAG QRAVLVGRSG SGKSSLLNAL SGFL SYQGS LRINGIELRD LSPESWRKHL SWVGQNPQLP AATLRDNVLL ARPDASEQEL QAALDNAWVS EFLPLLPQGV DTPVG DQAA RLSVGQAQRV AVARALLNPC SLLLLDQPAA SLDAHSEQRV MEALNAASLR QTTLMVTHQL EDLADWDVIW VMQDGR IIE QGRYAELSVA GGPFATLLAH RQEEI

UniProtKB: ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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 TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119296
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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