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- EMDB-18511: Mycobacterium smegmatis RNA polymerase in complex with HelD, SigA... -

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Basic information

Entry
Database: EMDB / ID: EMD-18511
TitleMycobacterium smegmatis RNA polymerase in complex with HelD, SigA and RbpA in State II
Map dataLoc-Scale filtered map
Sample
  • Complex: Mycobacterium smegmatis RNA polymerase in complex with HelD, SigA and RbpA in State II
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • Protein or peptide: RNA polymerase sigma factor SigA
    • Protein or peptide: Helicase
    • Protein or peptide: RNA polymerase-binding protein RbpA
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsHelD / RNA polymerase / transcription initiation / Mycobacteria / TRANSCRIPTION / rifampicin resistance
Function / homology
Function and homology information


recombinational repair / sigma factor activity / bacterial-type RNA polymerase core enzyme binding / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : ...recombinational repair / sigma factor activity / bacterial-type RNA polymerase core enzyme binding / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / hydrolase activity / protein dimerization activity / response to antibiotic / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
: / RNA polymerase-binding protein RbpA / RbpA superfamily / RNA polymerase-binding protein / UvrD/REP helicase N-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal ...: / RNA polymerase-binding protein RbpA / RbpA superfamily / RNA polymerase-binding protein / UvrD/REP helicase N-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit alpha / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit omega / RNA polymerase-binding protein RbpA / Helicase / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsKoval T / Krasny L / Dohnalek J / Kouba T
Funding support Czech Republic, European Union, 5 items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic23-06295S Czech Republic
Ministry of Education (MoE, Czech Republic)LM2023042 Czech Republic
Czech Academy of Sciences86652036 Czech Republic
Grant Agency of the Czech Republic23-06295S Czech Republic
European Union (EU)LX22NPO5103European Union
CitationJournal: Nat Commun / Year: 2024
Title: Mycobacterial HelD connects RNA polymerase recycling with transcription initiation.
Authors: Tomáš Kovaľ / Nabajyoti Borah / Petra Sudzinová / Barbora Brezovská / Hana Šanderová / Viola Vaňková Hausnerová / Alena Křenková / Martin Hubálek / Mária Trundová / Kristýna ...Authors: Tomáš Kovaľ / Nabajyoti Borah / Petra Sudzinová / Barbora Brezovská / Hana Šanderová / Viola Vaňková Hausnerová / Alena Křenková / Martin Hubálek / Mária Trundová / Kristýna Adámková / Jarmila Dušková / Marek Schwarz / Jana Wiedermannová / Jan Dohnálek / Libor Krásný / Tomáš Kouba /
Abstract: Mycobacterial HelD is a transcription factor that recycles stalled RNAP by dissociating it from nucleic acids and, if present, from the antibiotic rifampicin. The rescued RNAP, however, must ...Mycobacterial HelD is a transcription factor that recycles stalled RNAP by dissociating it from nucleic acids and, if present, from the antibiotic rifampicin. The rescued RNAP, however, must disengage from HelD to participate in subsequent rounds of transcription. The mechanism of release is unknown. We show that HelD from Mycobacterium smegmatis forms a complex with RNAP associated with the primary sigma factor σ and transcription factor RbpA but not CarD. We solve several structures of RNAP-σ-RbpA-HelD without and with promoter DNA. These snapshots capture HelD during transcription initiation, describing mechanistic aspects of HelD release from RNAP and its protective effect against rifampicin. Biochemical evidence supports these findings, defines the role of ATP binding and hydrolysis by HelD in the process, and confirms the rifampicin-protective effect of HelD. Collectively, these results show that when HelD is present during transcription initiation, the process is protected from rifampicin until the last possible moment.
History
DepositionSep 25, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18511.png

Downloads & links

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Map

FileDownload / File: emd_18511.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLoc-Scale filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 380 pix.
= 314.26 Å		0.83 Å/pix.
x 380 pix.
= 314.26 Å		0.83 Å/pix.
x 380 pix.
= 314.26 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.21529932 - 0.7252522
Average (Standard dev.)0.0028523328 (±0.024578119)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 314.26 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18511_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: RELION post-processed

Fileemd_18511_additional_1.map
AnnotationRELION post-processed
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18511_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18511_half_map_2.map
Projections & Slices
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Sample components

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Entire : Mycobacterium smegmatis RNA polymerase in complex with HelD, SigA...

EntireName: Mycobacterium smegmatis RNA polymerase in complex with HelD, SigA and RbpA in State II
Components
  • Complex: Mycobacterium smegmatis RNA polymerase in complex with HelD, SigA and RbpA in State II
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • Protein or peptide: RNA polymerase sigma factor SigA
    • Protein or peptide: Helicase
    • Protein or peptide: RNA polymerase-binding protein RbpA
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Mycobacterium smegmatis RNA polymerase in complex with HelD, SigA...

SupramoleculeName: Mycobacterium smegmatis RNA polymerase in complex with HelD, SigA and RbpA in State II
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Macromolecule #1: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 37.959441 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLISQRPTLS EETVAENRSR FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTDIILNL KGLVVSSDD DEPVTMYLRK QGPGVVTAGD IVPPAGVTVH NPDMHIATLN DKGKLEVELV VERGRGYVPA VQNKASGAEI G RIPVDSIY ...String:
MLISQRPTLS EETVAENRSR FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTDIILNL KGLVVSSDD DEPVTMYLRK QGPGVVTAGD IVPPAGVTVH NPDMHIATLN DKGKLEVELV VERGRGYVPA VQNKASGAEI G RIPVDSIY SPVLKVTYKV EATRVEQRTD FDKLIIDVET KNSISPRDAL ASAGGTLVEL FGLARELNAD SEHIEIGPSP AE ADHIASF ALPIDDLDLT VRSYNCLKRE GVHTVGELVA RTESDLLDIR NFGQKSIDEV KIKLHQLGLS LKDSPATFDP SEV AGYDAA TGTWTSDAGY DLDDNQDYAE TEQL

UniProtKB: DNA-directed RNA polymerase subunit alpha

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Macromolecule #2: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 128.680141 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLEGCILAVS SQSKSNAITN NSVPGAPNRV SFAKLREPLE VPGLLDVQTD SFEWLVGSDR WRQAAIDRGE ENPVGGLEEV LAELSPIED FSGSMSLSFS DPRFDEVKAS VDECKDKDMT YAAPLFVTAE FINNNTGEIK SQTVFMGDFP MMTEKGTFII N GTERVVVS ...String:
MLEGCILAVS SQSKSNAITN NSVPGAPNRV SFAKLREPLE VPGLLDVQTD SFEWLVGSDR WRQAAIDRGE ENPVGGLEEV LAELSPIED FSGSMSLSFS DPRFDEVKAS VDECKDKDMT YAAPLFVTAE FINNNTGEIK SQTVFMGDFP MMTEKGTFII N GTERVVVS QLVRSPGVYF DETIDKSTEK TLHSVKVIPG RGAWLEFDVD KRDTVGVRID RKRRQPVTVL LKALGWTNEQ IV ERFGFSE IMMGTLEKDT TSGTDEALLD IYRKLRPGEP PTKESAQTLL ENLFFKEKRY DLARVGRYKV NKKLGLNAGK PIT SSTLTE EDVVATIEYL VRLHEGQTSM TVPGGVEVPV EVDDIDHFGN RRLRTVGELI QNQIRVGLSR MERVVRERMT TQDV EAITP QTLINIRPVV AAIKEFFGTS QLSQFMDQNN PLSGLTHKRR LSALGPGGLS RERAGLEVRD VHPSHYGRMC PIETP EGPN IGLIGSLSVY ARVNPFGFIE TPYRKVENGV VTDQIDYLTA DEEDRHVVAQ ANSPTDENGR FTEDRVMVRK KGGEVE FVS ADQVDYMDVS PRQMVSVATA MIPFLEHDDA NRALMGANMQ RQAVPLVRSE APLVGTGMEL RAAIDAGDVV VADKTGV IE EVSADYITVM ADDGTRQSYR LRKFARSNHG TCANQRPIVD AGQRVEAGQV IADGPCTQNG EMALGKNLLV AIMPWEGH N YEDAIILSNR LVEEDVLTSI HIEEHEIDAR DTKLGAEEIT RDIPNVSDEV LADLDERGIV RIGAEVRDGD ILVGKVTPK GETELTPEER LLRAIFGEKA REVRDTSLKV PHGESGKVIG IRVFSREDDD ELPAGVNELV RVYVAQKRKI SDGDKLAGRH GNKGVIGKI LPVEDMPFLP DGTPVDIILN THGVPRRMNI GQILETHLGW VAKAGWNIDV AAGVPDWASK LPEELYSAPA D STVATPVF DGAQEGELAG LLGSTLPNRD GEVMVDADGK STLFDGRSGE PFPYPVTVGY MYILKLHHLV DDKIHARSTG PY SMITQQP LGGKAQFGGQ RFGEMECWAM QAYGAAYTLQ ELLTIKSDDT VGRVKVYEAI VKGENIPEPG IPESFKVLLK ELQ SLCLNV EVLSSDGAAI EMRDGDDEDL ERAAANLGIN LSRNESASVE DLA

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #3: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 146.712891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLDVNFFDEL RIGLATADDI RNWSYGEVKK PETINYRTLK PEKDGLFCEK IFGPTRDWEC YCGKYKRVRF KGIICERCGV EVTRAKVRR ERMGHIELAA PVTHIWYFKG VPSRLGYLLD LAPKDLEKII YFAAYVITSV DDEMRHNELS TLEAEMAVEK K AVEDQRDA ...String:
MLDVNFFDEL RIGLATADDI RNWSYGEVKK PETINYRTLK PEKDGLFCEK IFGPTRDWEC YCGKYKRVRF KGIICERCGV EVTRAKVRR ERMGHIELAA PVTHIWYFKG VPSRLGYLLD LAPKDLEKII YFAAYVITSV DDEMRHNELS TLEAEMAVEK K AVEDQRDA DLEARAQKLE ADLAELEAEG AKSDVRRKVR DSGEREMRQL RDRAQRELDR LDEIWNTFTK LAPKQLIVDE VL YRELQDR YGEYFTGAMG AESIKKLIEN FDIDAEAESL REVIRSGKGQ KKLRALKRLK VVAAFQQSGN SPMGMVLDAV PVI PPELRP MVQLDGGRFA TSDLNDLYRR VINRNNRLKR LIDLGAPEII VNNEKRMLQE SVDALFDNGR RGRPVTGPGN RPLK SLSDL LKGKQGRFRQ NLLGKRVDYS GRSVIVVGPQ LKLHQCGLPK LMALELFKPF VMKRLVDLNH AQNIKSAKRM VERQR PQVW DVLEEVIAEH PVLLNRAPTL HRLGIQAFEP QLVEGKAIQL HPLVCEAFNA DFDGDQMAVH LPLSAEAQAE ARILML SSN NILSPASGKP LAMPRLDMVT GLYYLTTLVE GATGEYQAAT KDAPEQGVYS SPAEAIMAMD RGALSVRAKI KVRLTEL RP PTDLEAQLFE NGWKPGDAWT AETTLGRVMF NELLPKSYPF VNEQMHKKVQ ARIINDLAER FPMIVVAQTV DKLKDAGF Y WATRSGVTVS MADVLVPPQK QEILERHEAE ADAIERKYQR GALNHTERNE SLVKIWQDAT EEVGKALEEF YPADNPIIT IVKSGATGNL TQTRTLAGMK GLVTNPKGEF IPRPIKSSFR EGLTVLEYFI NTHGARKGLA DTALRTADSG YLTRRLVDVS QDVIVREHD CETERGINVT LAERGPDGTL IRDAHVETSA FARTLATDAV DANGNVIIER GHDLGDPAID ALLAAGITTV K VRSVLTCT SATGVCAMCY GRSMATGKLV DIGEAVGIVA AQSIGEPGTQ LTMRTFHQGG VTGGADIVGG LPRVQELFEA RV PRNKAPI ADVAGRVRLE ESDKFFKITI VPDDGGEEVV YDKLSKRQRL RVITHEDGTE GVLSDGDHVE VGDQLMEGAA DPH EVLRVQ GPREVQIHLV KEVQEVYRAQ GVSIHDKHIE VIVRQMLRRV TIIDSGSTEF LPGSLTERAE FEAENRRVVA EGGE PAAGR PVLMGITKAS LATDSWLSAA SFQETTRVLT DAAINCRSDK LNGLKENVII GKLIPAGTGI SRYRNIQVQP TEEAR AAAY TIPSYEDQYY SPDFGQATGA AVPLDDYGYS DYR

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #4: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 11.544763 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSTPHADAQL NAADDLGIDS SAASAYDTPL GITNPPIDEL LSRASSKYAL VIYAAKRARQ INDYYNQLGD GILEYVGPLV EPGLQEKPL SIALREIHGD LLEHTEGE

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #5: RNA polymerase sigma factor SigA

MacromoleculeName: RNA polymerase sigma factor SigA / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 51.573551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAATKASPAT EEPVKRTATK TPAKKAPAKR AAKSAAAKAG GKAPAKKAPA KRAAKGTAAK PEDGVTDDLE VTDDLEAEPG EDLDVEDTD LELDDLDSDD DTAVEDEEEE ADAATPAVAT AKAADDDIDE PSEKDKASGD FVWDEEESEA LRQARKDAEL T ASADSVRA ...String:
MAATKASPAT EEPVKRTATK TPAKKAPAKR AAKSAAAKAG GKAPAKKAPA KRAAKGTAAK PEDGVTDDLE VTDDLEAEPG EDLDVEDTD LELDDLDSDD DTAVEDEEEE ADAATPAVAT AKAADDDIDE PSEKDKASGD FVWDEEESEA LRQARKDAEL T ASADSVRA YLKQIGKVAL LNAEEEVELA KRIEAGLYAT QKLAELAEKG EKLPVQQRRD MQWICRDGDR AKNHLLEANL RL VVSLAKR YTGRGMAFLD LIQEGNLGLI RAVEKFDYTK GYKFSTYATW WIRQAITRAM ADQARTIRIP VHMVEVINKL GRI QRELLQ DLGREPTPEE LAKEMDITPE KVLEIQQYAR EPISLDQTIG DEGDSQLGDF IEDSEAVVAV DAVSFTLLQD QLQS VLETL SEREAGVVRL RFGLTDGQPR TLDEIGQVYG VTRERIRQIE SKTMSKLRHP SRSQVLRDYL D

UniProtKB: RNA polymerase sigma factor SigA

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Macromolecule #6: Helicase

MacromoleculeName: Helicase / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 81.298078 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSGRDYEDEL QSERDYVAGL YARLDAERAQ SQRRYAAALR EHGGTAVERD AEVRALAKDI ARLNVADNGL CFGRLDTLDD ARLYIGRLG IFDRDNDFEP LLLDWRAPMA RPFYVATAAN PENMRRRRQF HTLGRKVVDF TDEILGRPTG AEHDATNDAA L LAAVNAPR ...String:
MSGRDYEDEL QSERDYVAGL YARLDAERAQ SQRRYAAALR EHGGTAVERD AEVRALAKDI ARLNVADNGL CFGRLDTLDD ARLYIGRLG IFDRDNDFEP LLLDWRAPMA RPFYVATAAN PENMRRRRQF HTLGRKVVDF TDEILGRPTG AEHDATNDAA L LAAVNAPR GEGMRDIVAT IQAEQDQVIR LDHTGVLVIE GGPGTGKTVV ALHRVAYLLY TYRKQMERHG VLVVGPTPAF LD HIGRVLP SLGESDAVFM TPGDFVPGLH VTAEDTPEAA EVKGSLKILD VLKAAVADRQ ELPSEPIPID LSDVTMRIDA ETA KWARDE ARKTGLPHNE ARAEFVDVVT YVVTERAVAR IGRGWLTRDD KHAWEKMRAD VVGELEDHEQ FNAALDALWP ILTP EDVLA QLYTSHERLR AAGAPECLWR ADGEAWTVSD VPLLDELVDL LGRNKAADEA AERERREEEA YAAGVLDLMV DREDL MDDE DHLLAQDLID AEELADRFKE QDNRELSERA AADREWTYGH VVVDEAQELS EMDWRLLMRR CPRRSFTIVG DLAQRR SPA GARSWGAMLD SYVPGRWVYK SLSVNYRTPA EIMAVAAAVL AEFAPDATPP DSVRACGVAP WARQVTDDDI ASAIAEF VS EEAGREGTSV VIGPPDVPGT VPPSETKGLE FDAVLVVEPE RILADGPRGA AELYVALTRA TQRLGVLYRD ALPQALAG L AEGDAAATVE QRTSA

UniProtKB: Helicase

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Macromolecule #7: RNA polymerase-binding protein RbpA

MacromoleculeName: RNA polymerase-binding protein RbpA / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 13.078731 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADRVLRGSR LGAVSYETDR NHDLAPRQVA RYRTDNGEEF DVPFADDAEI PGTWLCRNGL EGTLIEGDVP EPKKVKPPRT HWDMLLERR SVEELEELLK ERLDLIKAKR RGTGS

UniProtKB: RNA polymerase-binding protein RbpA

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6yxu

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57499
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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