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- EMDB-35993: Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the ca... -

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Basic information

Entry
Database: EMDB / ID: EMD-35993
TitleCryo-EM structure of Mycobacterium tuberculosis OppABCD in the catalytic intermediate state
Map data
Sample
  • Complex: Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the catalytic intermediate state
    • Protein or peptide: Uncharacterized protein Rv1280c
    • Protein or peptide: Putative peptide transport permease protein Rv1283c
    • Protein or peptide: Putative peptide transport permease protein Rv1282c
    • Protein or peptide: Uncharacterized ABC transporter ATP-binding protein Rv1281c
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: IRON/SULFUR CLUSTER
KeywordsOppABCD / ATP-Mg / Occluded state / Type I ABC importer / Membrane protein
Function / homology
Function and homology information


Tolerance by Mtb to nitric oxide produced by macrophages / glutathione binding / protein import / peptide transmembrane transporter activity / peptide transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / peptidoglycan-based cell wall / peptide binding / transmembrane transport ...Tolerance by Mtb to nitric oxide produced by macrophages / glutathione binding / protein import / peptide transmembrane transporter activity / peptide transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / peptidoglycan-based cell wall / peptide binding / transmembrane transport / protein transport / outer membrane-bounded periplasmic space / periplasmic space / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Oligopeptide transport permease C-like, N-terminal domain / N-terminal TM domain of oligopeptide transport permease C / ABC transporter type 1, GsiC-like, N-terminal domain / : / : / Binding-prot-dependent transport system membrane comp, N-term / Oligopeptide/dipeptide ABC transporter, C-terminal / Oligopeptide/dipeptide transporter, C-terminal region / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily ...Oligopeptide transport permease C-like, N-terminal domain / N-terminal TM domain of oligopeptide transport permease C / ABC transporter type 1, GsiC-like, N-terminal domain / : / : / Binding-prot-dependent transport system membrane comp, N-term / Oligopeptide/dipeptide ABC transporter, C-terminal / Oligopeptide/dipeptide transporter, C-terminal region / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / 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
Putative peptide transport permease protein Rv1283c / Putative peptide transport permease protein Rv1282c / Uncharacterized protein Rv1280c / Uncharacterized ABC transporter ATP-binding protein Rv1281c
Similarity search - Component
Biological speciesMycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsYang X / Hu T / Zhang B / Rao Z
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200996 China
National Natural Science Foundation of China (NSFC)32171217 China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: An oligopeptide permease, OppABCD, requires an iron-sulfur cluster domain for functionality.
Authors: Xiaolin Yang / Tianyu Hu / Jingxi Liang / Zhiqi Xiong / Zhenli Lin / Yao Zhao / Xiaoting Zhou / Yan Gao / Shan Sun / Xiuna Yang / Luke W Guddat / Haitao Yang / Zihe Rao / Bing Zhang /
Abstract: Oligopeptide permease, OppABCD, belongs to the type I ABC transporter family. Its role is to import oligopeptides into bacteria for nutrient uptake and to modulate the host immune response. OppABCD ...Oligopeptide permease, OppABCD, belongs to the type I ABC transporter family. Its role is to import oligopeptides into bacteria for nutrient uptake and to modulate the host immune response. OppABCD consists of a cluster C substrate-binding protein (SBP), OppA, membrane-spanning OppB and OppC subunits, and an ATPase, OppD, that contains two nucleotide-binding domains (NBDs). Here, using cryo-electron microscopy, we determined the high-resolution structures of Mycobacterium tuberculosis OppABCD in the resting state, oligopeptide-bound pre-translocation state, AMPPNP-bound pre-catalytic intermediate state and ATP-bound catalytic intermediate state. The structures show an assembly of a cluster C SBP with its ABC translocator and a functionally required [4Fe-4S] cluster-binding domain in OppD. Moreover, the ATP-bound OppABCD structure has an outward-occluded conformation, although no substrate was observed in the transmembrane cavity. Here, we reveal an oligopeptide recognition and translocation mechanism of OppABCD, which provides a perspective on how this and other type I ABC importers facilitate bulk substrate transfer across the lipid bilayer.
History
DepositionApr 24, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35993.png

Downloads & links

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Map

FileDownload / File: emd_35993.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.)
0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.0418918 - 2.9125967
Average (Standard dev.)0.003416351 (±0.07993295)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35993_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35993_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the ca...

EntireName: Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the catalytic intermediate state
Components
  • Complex: Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the catalytic intermediate state
    • Protein or peptide: Uncharacterized protein Rv1280c
    • Protein or peptide: Putative peptide transport permease protein Rv1283c
    • Protein or peptide: Putative peptide transport permease protein Rv1282c
    • Protein or peptide: Uncharacterized ABC transporter ATP-binding protein Rv1281c
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the ca...

SupramoleculeName: Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the catalytic intermediate state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)

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Macromolecule #1: Uncharacterized protein Rv1280c

MacromoleculeName: Uncharacterized protein Rv1280c / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Molecular weightTheoretical: 64.501113 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: VADRGQRRGC APGIASALRA SFQGKSRPWT QTRYWAFALL TPLVVAMVLT GCSASGTQLE LAPTADRRAA VGTTSDINQQ DPATLQDGG NLRLSLTDFP PNFNILHIDG NNAEVAAMMK ATLPRAFIIG PDGSTTVDTN YFTSIELTRT APQVVTYTIN P EAVWSDGT ...String:
VADRGQRRGC APGIASALRA SFQGKSRPWT QTRYWAFALL TPLVVAMVLT GCSASGTQLE LAPTADRRAA VGTTSDINQQ DPATLQDGG NLRLSLTDFP PNFNILHIDG NNAEVAAMMK ATLPRAFIIG PDGSTTVDTN YFTSIELTRT APQVVTYTIN P EAVWSDGT PITWRDIASQ IHAISGADKA FEIASSSGAE RVASVTRGVD DRQAVVTFAK PYAEWRGMFA GNGMLLPASM TA TPEAFNK GQLDGPGPSA GPFVVSALDR TAQRIVLTRN PRWWGARPRL DSITYLVLDD AARLPALQNN TIDATGVGTL DQL TIAART KGISIRRAPG PSWYHFTLNG APGSILADKA LRLAIAKGID RYTIARVAQY GLTSDPVPLN NHVFVAGQDG YQDN SGVVA YNPEQAKREL DALGWRRSGA FREKDGRQLV IRDLFYDAQS TRQFAQIAQH TLAQIGVKLE LQAKSGSGFF SDYVN VGAF DIAQFGWVGD AFPLSSLTQI YASDGESNFG KIGSPQIDAA IERTLAELDP GKARALANQV DELIWAEGFS LPLTQS PGT VAVRSTLANF GATGLADLDY TAIGFMRRDY KDDDDK

UniProtKB: Uncharacterized protein Rv1280c

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Macromolecule #2: Putative peptide transport permease protein Rv1283c

MacromoleculeName: Putative peptide transport permease protein Rv1283c / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Molecular weightTheoretical: 35.120133 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MTRYLARRLL NYLVLLALAS FLTYCLTSLA FSPLESLMQR SPRPPQAVID AKAHDLGLDR PILARYANWV SHAVRGDFGT TITGQPVGT ELGRRIGVSL RLLVVGSVFG TVAGVVIGAW GAIRQYRLSD RVMTTLALLV LSTPTFVVAN LLILGALRVN W AVGIQLFD ...String:
MTRYLARRLL NYLVLLALAS FLTYCLTSLA FSPLESLMQR SPRPPQAVID AKAHDLGLDR PILARYANWV SHAVRGDFGT TITGQPVGT ELGRRIGVSL RLLVVGSVFG TVAGVVIGAW GAIRQYRLSD RVMTTLALLV LSTPTFVVAN LLILGALRVN W AVGIQLFD YTGETSPGVA GGVWDRLGDR LQHLILPSLT LALAAAAGFS RYQRNAMLDV LGQDFIRTAR AKGLTRRRAL LK HGLRTAL IPMATLFAYG VAGLVTGAVF VEKIFGWHGM GEWMVRGIST QDTNIVAAIT VFSGAVVLLA GLLSDVIYAA LDP RVRVS

UniProtKB: Putative peptide transport permease protein Rv1283c

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Macromolecule #3: Putative peptide transport permease protein Rv1282c

MacromoleculeName: Putative peptide transport permease protein Rv1282c / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Molecular weightTheoretical: 31.402119 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MTEFASRRTL VVRRFLRNRA AVASLAALLL LFVSAYALPP LLPYSYDDLD FNALLQPPGT KHWLGTNALG QDLLAQTLRG MQKSMLIGV CVAVISTGIA ATVGAISGYF GGWRDRTLMW VVDLLLVVPS FILIAIVTPR TKNSANIMFL VLLLAGFGWM I SSRMVRGM ...String:
MTEFASRRTL VVRRFLRNRA AVASLAALLL LFVSAYALPP LLPYSYDDLD FNALLQPPGT KHWLGTNALG QDLLAQTLRG MQKSMLIGV CVAVISTGIA ATVGAISGYF GGWRDRTLMW VVDLLLVVPS FILIAIVTPR TKNSANIMFL VLLLAGFGWM I SSRMVRGM TMSLREREFI RAARYMGVSS RRIIVGHVVP NVASILIIDA ALNVAAAILA ETGLSFLGFG IQPPDVSLGT LI ADGTASA TAFPWVFLFP ASILVLILVC ANLTGDGLRD ALDPASRSLR RGVR

UniProtKB: Putative peptide transport permease protein Rv1282c

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Macromolecule #4: Uncharacterized ABC transporter ATP-binding protein Rv1281c

MacromoleculeName: Uncharacterized ABC transporter ATP-binding protein Rv1281c
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Molecular weightTheoretical: 65.342793 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MSPLLEVTDL AVTFRTDGDP VTAVRGISYR VEPGEVVAMV GESGSGKSAA AMAVVGLLPE YAQVRGSVRL QGTELLGLAD NAMSRFRGK AIGTVFQDPM SALTPVYTVG DQIAEAIEVH QPRVGKKAAR RRAVELLDLV GISQPQRRSR AFPHELSGGE R QRVVIAIA ...String:
MSPLLEVTDL AVTFRTDGDP VTAVRGISYR VEPGEVVAMV GESGSGKSAA AMAVVGLLPE YAQVRGSVRL QGTELLGLAD NAMSRFRGK AIGTVFQDPM SALTPVYTVG DQIAEAIEVH QPRVGKKAAR RRAVELLDLV GISQPQRRSR AFPHELSGGE R QRVVIAIA IANDPDLLIC DDPTTALDVT VQAQILDVLK AARDVTGAGV LIITHDLGVV AEFADRALVM YAGRVVESAG VN DLYRDRR MPYTVGLLGS VPRLDAAQGT RLVPIPGAPP SLAGLAPGCP FAPRCPLVID ECLTAEPELL DVATDHRAAC IRT ELVTGR SAADIYRVKT EARPAALGDA SVVVRVRHLV KTYRLAKGVV LRRAIGEVRA VDGISLELRQ GRTLGIVGES GSGK STTLH EILELAAPQS GSIEVLGTDV ATLGTAERRS LRRDIQVVFQ DPVASLDPRL PVFDLIAEPL QANGFGKNET HARVA ELLD IVGLRHGDAS RYPAEFSGGQ KQRIGIARAL ALQPKILALD DPVSALDVSI QAGIINLLLD LQEQFGLSYL FVSHDL SVV KHLAHQVAVM LAGTVVEQGD SEEVFGNPKH EYTRRLLGAV PQPDPARRG

UniProtKB: Uncharacterized ABC transporter ATP-binding protein Rv1281c

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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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
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: 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: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60489
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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