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- EMDB-35991: Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the re... -
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Open data
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Basic information
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Title | Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the resting state | |||||||||
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![]() | OppABCD / Type I ABC importer / Oligopeptide permease / ![]() ![]() | |||||||||
Function / homology | ![]() Tolerance by Mtb to nitric oxide produced by macrophages / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Yang X / Hu T / Zhang B / Rao Z | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 154.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.9 KB 18.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.2 KB | Display | ![]() |
Images | ![]() | 50.6 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() | 151.9 MB 151.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8j5rMC ![]() 8j5qC ![]() 8j5sC ![]() 8j5tC ![]() 8j5uC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_35991_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35991_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the re...
Entire | Name: Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the resting state |
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Components |
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-Supramolecule #1: Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the re...
Supramolecule | Name: Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the resting state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Uncharacterized protein Rv1280c
Macromolecule | Name: Uncharacterized protein Rv1280c / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 64.38598 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 DIAQFGAVGD AFPLSSLTQI YASDGESNFG KIGSPQIDAA IERTLAELDP GKARALANQV DELIWAEGFS LPLTQS PGT VAVRSTLANF GATGLADLDY TAIGFMRRDY KDDDDK UniProtKB: Uncharacterized protein Rv1280c |
-Macromolecule #2: Putative peptide transport permease protein Rv1283c
Macromolecule | Name: Putative peptide transport permease protein Rv1283c / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 35.120133 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #3: Putative peptide transport permease protein Rv1282c
Macromolecule | Name: Putative peptide transport permease protein Rv1282c / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 31.402119 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #4: Uncharacterized ABC transporter ATP-binding protein Rv1281c
Macromolecule | Name: Uncharacterized ABC transporter ATP-binding protein Rv1281c type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 65.370848 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 DEPTTALDVT 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 EPVSALDVSI QAGIINLLLD LQEQFGLSYL FVSHDL SVV KHLAHQVAVM LAGTVVEQGD SEEVFGNPKH EYTRRLLGAV PQPDPARRG UniProtKB: Uncharacterized ABC transporter ATP-binding protein Rv1281c |
-Macromolecule #5: IRON/SULFUR CLUSTER
Macromolecule | Name: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: SF4 |
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Molecular weight | Theoretical: 351.64 Da |
Chemical component information | ![]() ChemComp-FS1: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |