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- EMDB-13004: Pol II-CSB-CSA-DDB1-UVSSA (Structure1) -

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Basic information

Entry
Database: EMDB / ID: EMD-13004
TitlePol II-CSB-CSA-DDB1-UVSSA (Structure1)
Map dataMain map.
Sample
  • Complex: RNA polymerase II elongation complex with CSB, CSA-DDB1 and UVSSA.
    • Complex: DNA directed RNA polymerase
      • Protein or peptide: x 12 types
    • Complex: NTS, TS & RNA
      • DNA: x 2 types
      • RNA: x 1 types
    • Complex: DNA Repair proteins, CSB element and scaffold protein
      • Protein or peptide: x 5 types
  • Ligand: x 2 types
Keywordstranscription / DNA repair
Function / homology
Function and homology information


negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / : / regulation of transcription elongation by RNA polymerase II / DNA protection / B-WICH complex / single strand break repair / positive regulation by virus of viral protein levels in host cell / Formation of RNA Pol II elongation complex ...negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / : / regulation of transcription elongation by RNA polymerase II / DNA protection / B-WICH complex / single strand break repair / positive regulation by virus of viral protein levels in host cell / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / double-strand break repair via classical nonhomologous end joining / response to superoxide / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / ATP-dependent chromatin remodeler activity / photoreceptor cell maintenance / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / positive regulation of DNA-templated transcription, elongation / response to UV-B / RNA polymerase binding / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / positive regulation of transcription by RNA polymerase III / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / organelle membrane / positive regulation of transcription by RNA polymerase I / negative regulation of reproductive process / negative regulation of developmental process / RNA polymerase II complex binding / cullin family protein binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / viral release from host cell / site of DNA damage / protein tyrosine kinase activator activity / RNA Polymerase I Transcription Initiation / positive regulation of translational initiation / pyrimidine dimer repair / ATP-dependent activity, acting on DNA / positive regulation of transcription initiation by RNA polymerase II / response to X-ray / ectopic germ cell programmed cell death / transcription by RNA polymerase III / transcription by RNA polymerase I / positive regulation of double-strand break repair via homologous recombination / RNA polymerase I complex / transcription elongation by RNA polymerase I / positive regulation of viral genome replication / RNA polymerase III complex / proteasomal protein catabolic process / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / response to UV / : / protein autoubiquitination / JNK cascade / translation initiation factor binding / neurogenesis / positive regulation of gluconeogenesis / DNA-directed RNA polymerase activity / positive regulation of DNA repair / positive regulation of RNA splicing / DNA damage checkpoint signaling / transcription elongation factor complex / regulation of DNA-templated transcription elongation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / response to gamma radiation / helicase activity / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / P-body / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER
Similarity search - Function
UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / : / RNA-binding domain, S1 / ENTH/VHS / RSE1/DDB1/CPSF1 second beta-propeller ...UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / : / RNA-binding domain, S1 / ENTH/VHS / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / 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
Similarity search - Domain/homology
RNA polymerase II subunit D / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase II subunit E ...RNA polymerase II subunit D / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase II subunit E / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB9 / DNA excision repair protein ERCC-6 / DNA excision repair protein ERCC-8 / DNA damage-binding protein 1 / UV-stimulated scaffold protein A
Similarity search - Component
Biological speciesSus scrofa (pig) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKokic G / Cramer P
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2067/1 39072994, SFB860, SPP2191 Germany
European Research Council (ERC)882357 Germany
CitationJournal: Nature / Year: 2021
Title: Structural basis of human transcription-DNA repair coupling.
Authors: Goran Kokic / Felix R Wagner / Aleksandar Chernev / Henning Urlaub / Patrick Cramer /
Abstract: Transcription-coupled DNA repair removes bulky DNA lesions from the genome and protects cells against ultraviolet (UV) irradiation. Transcription-coupled DNA repair begins when RNA polymerase II ...Transcription-coupled DNA repair removes bulky DNA lesions from the genome and protects cells against ultraviolet (UV) irradiation. Transcription-coupled DNA repair begins when RNA polymerase II (Pol II) stalls at a DNA lesion and recruits the Cockayne syndrome protein CSB, the E3 ubiquitin ligase, CRL4 and UV-stimulated scaffold protein A (UVSSA). Here we provide five high-resolution structures of Pol II transcription complexes containing human transcription-coupled DNA repair factors and the elongation factors PAF1 complex (PAF) and SPT6. Together with biochemical and published data, the structures provide a model for transcription-repair coupling. Stalling of Pol II at a DNA lesion triggers replacement of the elongation factor DSIF by CSB, which binds to PAF and moves upstream DNA to SPT6. The resulting elongation complex, EC, uses the CSA-stimulated translocase activity of CSB to pull on upstream DNA and push Pol II forward. If the lesion cannot be bypassed, CRL4 spans over the Pol II clamp and ubiquitylates the RPB1 residue K1268, enabling recruitment of TFIIH to UVSSA and DNA repair. Conformational changes in CRL4 lead to ubiquitylation of CSB and to release of transcription-coupled DNA repair factors before transcription may continue over repaired DNA.
History
DepositionMay 26, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
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  • Surface view colored by radius
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  • Surface view with fitted model
  • Atomic models: PDB-7oo3
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13004.png

Downloads & links

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Map

FileDownload / File: emd_13004.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map.
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
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Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.10523341 - 0.18084967
Average (Standard dev.)-0.0004728839 (±0.0031010401)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z420.000420.000420.000
α/β/γ90.00090.00090.000
start NX/NY/NZ29290
NX/NY/NZ140137200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1050.181-0.000

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Supplemental data

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Mask #1

Fileemd_13004_msk_1.map
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Mask #2

Fileemd_13004_msk_2.map
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Mask #3

Fileemd_13004_msk_3.map
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Mask #4

Fileemd_13004_msk_4.map
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Mask #5

Fileemd_13004_msk_5.map
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Additional map: Half map corresponding to the map focused refined on CSA-UVSSA.

Fileemd_13004_additional_1.map
AnnotationHalf map corresponding to the map focused refined on CSA-UVSSA.
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Additional map: Half map corresponding to the map focused refined on CSA-UVSSA.

Fileemd_13004_additional_10.map
AnnotationHalf map corresponding to the map focused refined on CSA-UVSSA.
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Additional map: Half map corresponding to the map focused refined on CSB.

Fileemd_13004_additional_2.map
AnnotationHalf map corresponding to the map focused refined on CSB.
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Additional map: Half map corresponding to the map focused refined on CSA-DDB1.

Fileemd_13004_additional_3.map
AnnotationHalf map corresponding to the map focused refined on CSA-DDB1.
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Additional map: Half map corresponding to the map focused refined on CSB.

Fileemd_13004_additional_4.map
AnnotationHalf map corresponding to the map focused refined on CSB.
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Additional map: Half map corresponding to the map focused refined on CSA-DDB1.

Fileemd_13004_additional_5.map
AnnotationHalf map corresponding to the map focused refined on CSA-DDB1.
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Additional map: Half map corresponding to the map focused refined on DDB1.

Fileemd_13004_additional_6.map
AnnotationHalf map corresponding to the map focused refined on DDB1.
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Additional map: Half map corresponding to the map focused refined on DDB1.

Fileemd_13004_additional_7.map
AnnotationHalf map corresponding to the map focused refined on DDB1.
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Additional map: Half map corresponding to the map focused refined on Pol II.

Fileemd_13004_additional_8.map
AnnotationHalf map corresponding to the map focused refined on Pol II.
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Additional map: Half map corresponding to the map focused refined on Pol II.

Fileemd_13004_additional_9.map
AnnotationHalf map corresponding to the map focused refined on Pol II.
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Half map: Half map corresponding to the main map.

Fileemd_13004_half_map_1.map
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Half map: Half map corresponding to the main map.

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Sample components

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Entire : RNA polymerase II elongation complex with CSB, CSA-DDB1 and UVSSA.

EntireName: RNA polymerase II elongation complex with CSB, CSA-DDB1 and UVSSA.
Components
  • Complex: RNA polymerase II elongation complex with CSB, CSA-DDB1 and UVSSA.
    • Complex: DNA directed RNA polymerase
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB1
      • Protein or peptide: DNA-directed RNA polymerase subunit beta
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB3
      • Protein or peptide: RPOL4c domain-containing protein
      • Protein or peptide: DNA-directed RNA polymerase II subunit E
      • Protein or peptide: DNA-directed RNA polymerase II subunit F
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB7
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB9
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5
      • Protein or peptide: RNA_pol_L_2 domain-containing protein
      • Protein or peptide: RNA polymerase II subunit K
    • Complex: NTS, TS & RNA
      • DNA: NTS
      • DNA: TS
      • RNA: RNA
    • Complex: DNA Repair proteins, CSB element and scaffold protein
      • Protein or peptide: DNA excision repair protein ERCC-8
      • Protein or peptide: DNA excision repair protein ERCC-6
      • Protein or peptide: CSB element
      • Protein or peptide: UV-stimulated scaffold protein A
      • Protein or peptide: DNA damage-binding protein 1
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: RNA polymerase II elongation complex with CSB, CSA-DDB1 and UVSSA.

SupramoleculeName: RNA polymerase II elongation complex with CSB, CSA-DDB1 and UVSSA.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20

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Supramolecule #2: DNA directed RNA polymerase

SupramoleculeName: DNA directed RNA polymerase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#12
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #3: NTS, TS & RNA

SupramoleculeName: NTS, TS & RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #13-#15
Source (natural)Organism: Homo sapiens (human) / Synthetically produced: Yes

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Supramolecule #4: DNA Repair proteins, CSB element and scaffold protein

SupramoleculeName: DNA Repair proteins, CSB element and scaffold protein / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #16-#20
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 217.450078 KDa
SequenceString: MHGGGPPSGD SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP RQGVIERTGR CQTCAGNMTE CPGHFGHIE LAKPVFHVGF LVKTMKVLRC VCFFCSKLLV DSNNPKIKDI LAKSKGQPKK RLTHVYDLCK GKNICEGGEE M DNKFGVEQ ...String:
MHGGGPPSGD SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP RQGVIERTGR CQTCAGNMTE CPGHFGHIE LAKPVFHVGF LVKTMKVLRC VCFFCSKLLV DSNNPKIKDI LAKSKGQPKK RLTHVYDLCK GKNICEGGEE M DNKFGVEQ PEGDEDLTKE KGHGGCGRYQ PRIRRSGLEL YAEWKHVNED SQEKKILLSP ERVHEIFKRI SDEECFVLGM EP RYARPEW MIVTVLPVPP LSVRPAVVMQ GSARNQDDLT HKLADIVKIN NQLRRNEQNG AAAHVIAEDV KLLQFHVATM VDN ELPGLP RAMQKSGRPL KSLKQRLKGK EGRVRGNLMG KRVDFSARTV ITPDPNLSID QVGVPRSIAA NMTFAEIVTP FNID RLQEL VRRGNSQYPG AKYIIRDNGD RIDLRFHPKP SDLHLQTGYK VERHMCDGDI VIFNRQPTLH KMSMMGHRVR ILPWS TFRL NLSVTTPYNA DFDGDEMNLH LPQSLETRAE IQELAMVPRM IVTPQSNRPV MGIVQDTLTA VRKFTKRDVF LERGEV MNL LMFLSTWDGK VPQPAILKPR PLWTGKQIFS LIIPGHINCI RTHSTHPDDE DSGPYKHISP GDTKVVVENG ELIMGIL CK KSLGTSAGSL VHISYLEMGH DITRLFYSNI QTVINNWLLI EGHTIGIGDS IADSKTYQDI QNTIKKAKQD VIEVIEKA H NNELEPTPGN TLRQTFENQV NRILNDARDK TGSSAQKSLS EYNNFKSMVV SGAKGSKINI SQVIAVVGQQ NVEGKRIPF GFKHRTLPHF IKDDYGPESR GFVENSYLAG LTPTEFFFHA MGGREGLIDT AVKTAETGYI QRRLIKSMES VMVKYDATVR NSINQVVQL RYGEDGLAGE SVEFQNLATL KPSNKAFEKK FRFDYTNERA LRRTLQEDLV KDVLSNAHIQ NELEREFERM R EDREVLRV IFPTGDSKVV LPCNLLRMIW NAQKIFHINP RLPSDLHPIK VVEGVKELSK KLVIVNGDDP LSRQAQENAT LL FNIHLRS TLCSRRMAEE FRLSGEAFDW LLGEIESKFN QAIAHPGEMV GALAAQSLGE PATQMTLNTF HYAGVSAKNV TLG VPRLKE LINISKKPKT PSLTVFLLGQ SARDAERAKD ILCRLEHTTL RKVTANTAIY YDPNPQSTVV AEDQEWVNVY YEMP DFDVA RISPWLLRVE LDRKHMTDRK LTMEQIAEKI NAGFGDDLNC IFNDDNAEKL VLRIRIMNSD ENKMQEEEEV VDKMD DDVF LRCIESNMLT DMTLQGIEQI SKVYMHLPQT DNKKKIIITE DGEFKALQEW ILETDGVSLM RVLSEKDVDP VRTTSN DIV EIFTVLGIEA VRKALERELY HVISFDGSYV NYRHLALLCD TMTCRGHLMA ITRHGVNRQD TGPLMKCSFE ETVDVLM EA AAHGESDPMK GVSENIMLGQ LAPAGTGCFD LLLDAEKCKY GMEIPTNIPG LGAAGPTGMF FGSAPSPMGG ISPAMTPW N QGATPAYGAW SPSVGSGMTP GAAGFSPSAA SDASGFSPGY SPAWSPTPGS PGSPGPSSPY IPSPGGAMSP SYSPTSPAY EPRSPGGYTP QSPSYSPTSP SYSPTSPSYS PTSPNYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPNYS PTSPNYTPTS P SYSPTSPS YSPTSPNYTP TSPNYSPTSP SYSPTSPSYS PTSPSYSPSS PRYTPQSPTY TPSSPSYSPS SPSYSPTSPK YT PTSPSYS PSSPEYTPTS PKYSPTSPKY SPTSPKYSPT SPTYSPTTPK YSPTSPTYSP TSPVYTPTSP KYSPTSPTYS PTS PKYSPT SPTYSPTSPK GSTYSPTSPG YSPTSPTYSL TSPAISPDDS DEEN

UniProtKB: DNA-directed RNA polymerase II subunit RPB1

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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: Sus scrofa (pig)
Molecular weightTheoretical: 134.041422 KDa
SequenceString: MYDADEDMQY DEDDDEITPD LWQEACWIVI SSYFDEKGLV RQQLDSFDEF IQMSVQRIVE DAPPIDLQAE AQHASGEVEE PPRYLLKFE QIYLSKPTHW ERDGAPSPMM PNEARLRNLT YSAPLYVDIT KTVIKEGEEQ LQTQHQKTFI GKIPIMLRST Y CLLNGLTD ...String:
MYDADEDMQY DEDDDEITPD LWQEACWIVI SSYFDEKGLV RQQLDSFDEF IQMSVQRIVE DAPPIDLQAE AQHASGEVEE PPRYLLKFE QIYLSKPTHW ERDGAPSPMM PNEARLRNLT YSAPLYVDIT KTVIKEGEEQ LQTQHQKTFI GKIPIMLRST Y CLLNGLTD RDLCELNECP LDPGGYFIIN GSEKVLIAQE KMATNTVYVF AKKDSKYAYT GECRSCLENS SRPTSTIWVS ML ARGGQGA KKSAIGQRIV ATLPYIKQEV PIIIVFRALG FVSDRDILEH IIYDFEDPEM MEMVKPSLDE AFVIQEQNVA LNF IGSRGA KPGVTKEKRI KYAKEVLQKE MLPHVGVSDF CETKKAYFLG YMVHRLLLAA LGRRELDDRD HYGNKRLDLA GPLL AFLFR GMFKNLLKEV RIYAQKFIDR GKDFNLELAI KTRIISDGLK YSLATGNWGD QKKAHQARAG VSQVLNRLTF ASTLS HLRR LNSPIGRDGK LAKPRQLHNT LWGMVCPAET PEGHAVGLVK NLALMAYISV GSQPSPILEF LEEWSMENLE EISPAA IAD ATKIFVNGCW VGIHKDPEQL MNTLRKLRRQ MDIIVSEVSM IRDIREREIR IYTDAGRICR PLLIVEKQKL LLKKRHI DQ LKEREYNNYS WQDLVASGVV EYIDTLEEET VMLAMTPDDL QEKEVAYCST YTHCEIHPSM ILGVCASIIP FPDHNQSP R NTYQSAMGKQ AMGVYITNFH VRMDTLAHVL YYPQKPLVTT RSMEYLRFRE LPAGINSIVA IASYTGYNQE DSVIMNRSA VDRGFFRSVF YRSYKEQESK KGFDQEEVFE KPTRETCQGM RHAIYDKLDD DGLIAPGVRV SGDDVIIGKT VTLPENEDEL EGTNRRYTK RDCSTFLRTS ETGIVDQVMV TLNQEGYKFC KIRVRSVRIP QIGDKFASRH GQKGTCGIQY RQEDMPFTCE G ITPDIIIN PHAIPSRMTI GHLIECLQGK VSANKGEIGD ATPFNDAVNV QKISNLLSDY GYHLRGNEVL YNGFTGRKIT SQ IFIGPTY YQRLKHMVDD KIHSRARGPI QILNRQPMEG RSRDGGLRFG EMERDCQIAH GAAQFLRERL FEASDPYQVH VCN LCGIMA IANTRTHTYE CRGCRNKTQI SLVRMPYACK LLFQELMSMS IAPRMMSV

UniProtKB: DNA-directed RNA polymerase subunit beta

+
Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 31.439074 KDa
SequenceString: MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH DEFIAHRLGL IPLTSDDIVD KLQYSRDCT CEEFCPECSV EFTLDVRCNE DQTRHVTSRD LISNSPRVIP VTSRNRDNDP SDYVEQDDIL IVKLRKGQEL R LRAYAKKG ...String:
MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH DEFIAHRLGL IPLTSDDIVD KLQYSRDCT CEEFCPECSV EFTLDVRCNE DQTRHVTSRD LISNSPRVIP VTSRNRDNDP SDYVEQDDIL IVKLRKGQEL R LRAYAKKG FGKEHAKWNP TAGVAFEYDP DNALRHTVYP KPEEWPKSEY SELDEDESQA PYDPNGKPER FYYNVESCGS LR PETIVLS ALSGLKKKLS DLQTQLSHEI QSDVLTIN

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

+
Macromolecule #4: RPOL4c domain-containing protein

MacromoleculeName: RPOL4c domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 16.331255 KDa
SequenceString:
MAAGGSDPRA GDVEEDASQL IFPKEFETAE TLLNSEVHML LEHRKQQNES AEDEQELSEV FMKTLNYTAR FSRFKNRETI ASVRSLLLQ KKLHKFELAC LANLCPETAE ESKALIPSLE GRFEDEELQQ ILDDIQTKRS FQY

UniProtKB: RNA polymerase II subunit D

+
Macromolecule #5: DNA-directed RNA polymerase II subunit E

MacromoleculeName: DNA-directed RNA polymerase II subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 24.644318 KDa
SequenceString: MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQFGDKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV DMAPKYILEQ FLQQELLINI TEHELVPEHV VMTKEEVTEL L ARYKLREN ...String:
MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQFGDKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV DMAPKYILEQ FLQQELLINI TEHELVPEHV VMTKEEVTEL L ARYKLREN QLPRIQAGDP VARYFGIKRG QVVKIIRPSE TAGRYITYRL VQ

UniProtKB: DNA-directed RNA polymerase II subunit E

+
Macromolecule #6: DNA-directed RNA polymerase II subunit F

MacromoleculeName: DNA-directed RNA polymerase II subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 14.477001 KDa
SequenceString:
MSDNEDNFDG DDFDDVEEDE GLDDLENAEE EGQENVEILP SGERPQANQK RITTPYMTKY ERARVLGTRA LQIAMCAPVM VELEGETDP LLIAMKELKA RKIPIIIRRY LPDGSYEDWG VDELIISD

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC2

+
Macromolecule #7: DNA-directed RNA polymerase II subunit RPB7

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 19.314283 KDa
SequenceString:
MFYHISLEHE ILLHPRYFGP NLLNTVKQKL FTEVEGTCTG KYGFVIAVTT IDNIGAGVIQ PGRGFVLYPV KYKAIVFRPF KGEVVDAVV TQVNKVGLFT EIGPMSCFIS RHSIPSEMEF DPNSNPPCYK TMDEDIVIQQ DDEIRLKIVG TRVDKNDIFA I GSLMDDYL GLVS

UniProtKB: DNA-directed RNA polymerase II subunit RPB7

+
Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC3
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 17.162273 KDa
SequenceString:
MAGILFEDIF DVKDIDPEGK KFDRVSRLHC ESESFKMDLI LDVNIQIYPV DLGDKFRLVI ASTLYEDGTL DDGEYNPTDD RPSRADQFE YVMYGKVYRI EGDETSTEAA TRLSAYVSYG GLLMRLQGDA NNLHGFEVDS RVYLLMKKLA F

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC3

+
Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 14.541221 KDa
SequenceString:
MEPDGTYEPG FVGIRFCQEC NNMLYPKEDK ENRILLYACR NCDYQQEADN SCIYVNKITH EVDELTQIIA DVSQDPTLPR TEDHPCQKC GHKEAVFFQS HSARAEDAMR LYYVCTAPHC GHRWTE

UniProtKB: DNA-directed RNA polymerase II subunit RPB9

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Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC5
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 7.655123 KDa
SequenceString:
MIIPVRCFTC GKIVGNKWEA YLGLLQAEYT EGDALDALGL KRYCCRRMLL AHVDLIEKLL NYAPLEK

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC5

+
Macromolecule #11: RNA_pol_L_2 domain-containing protein

MacromoleculeName: RNA_pol_L_2 domain-containing protein / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 13.310284 KDa
SequenceString:
MNAPPAFESF LLFEGEKKIT INKDTKVPNA CLFTINKEDH TLGNIIKSQL LKDPQVLFAG YKVPHPLEHK IIIRVQTTPD YSPQEAFTN AITDLISELS LLEERFRVAI KDKQEGIE

UniProtKB: DNA-directed RNA polymerase II subunit RPB11-a

+
Macromolecule #12: RNA polymerase II subunit K

MacromoleculeName: RNA polymerase II subunit K / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 7.018244 KDa
SequenceString:
MDTQKDVQPP KQQPMIYICG ECHTENEIKS RDPIRCRECG YRIMYKKRTK RLVVFDAR

UniProtKB: RNA polymerase II, I and III subunit K

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Macromolecule #16: DNA excision repair protein ERCC-8

MacromoleculeName: DNA excision repair protein ERCC-8 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.10716 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MLGFLSARQT GLEDPLRLRR AESTRRVLGL ELNKDRDVER IHGGGINTLD IEPVEGRYML SGGSDGVIVL YDLENSSRQS YYTCKAVCS IGRDHPDVHR YSVETVQWYP HDTGMFTSSS FDKTLKVWDT NTLQTADVFN FEETVYSHHM SPVSTKHCLV A VGTRGPKV ...String:
MLGFLSARQT GLEDPLRLRR AESTRRVLGL ELNKDRDVER IHGGGINTLD IEPVEGRYML SGGSDGVIVL YDLENSSRQS YYTCKAVCS IGRDHPDVHR YSVETVQWYP HDTGMFTSSS FDKTLKVWDT NTLQTADVFN FEETVYSHHM SPVSTKHCLV A VGTRGPKV QLCDLKSGSC SHILQGHRQE ILAVSWSPRY DYILATASAD SRVKLWDVRR ASGCLITLDQ HNGKKSQAVE SA NTAHNGK VNGLCFTSDG LHLLTVGTDN RMRLWNSSNG ENTLVNYGKV CNNSKKGLKF TVSCGCSSEF VFVPYGSTIA VYT VYSGEQ ITMLKGHYKT VDCCVFQSNF QELYSGSRDC NILAWVPSLY EPVPDDDETT TKSQLNPAFE DAWSSSDEEG

UniProtKB: DNA excision repair protein ERCC-8

+
Macromolecule #17: DNA excision repair protein ERCC-6

MacromoleculeName: DNA excision repair protein ERCC-6 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 168.673547 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPNEGIPHSS QTQEQDCLQS QPVSNNEEMA IKQESGGDGE VEEYLSFRSV GDGLSTSAVG CASAAPRRGP ALLHIDRHQI QAVEPSAQA LELQGLGVDV YDQDVLEQGV LQQVDNAIHE ASRASQLVDV EKEYRSVLDD LTSCTTSLRQ INKIIEQLSP Q AATSRDIN ...String:
MPNEGIPHSS QTQEQDCLQS QPVSNNEEMA IKQESGGDGE VEEYLSFRSV GDGLSTSAVG CASAAPRRGP ALLHIDRHQI QAVEPSAQA LELQGLGVDV YDQDVLEQGV LQQVDNAIHE ASRASQLVDV EKEYRSVLDD LTSCTTSLRQ INKIIEQLSP Q AATSRDIN RKLDSVKRQK YNKEQQLKKI TAKQKHLQAI LGGAEVKIEL DHASLEEDAE PGPSSLGSML MPVQETAWEE LI RTGQMTP FGTQIPQKQE KKPRKIMLNE ASGFEKYLAD QAKLSFERKK QGCNKRAARK APAPVTPPAP VQNKNKPNKK ARV LSKKEE RLKKHIKKLQ KRALQFQGKV GLPKARRPWE SDMRPEAEGD SEGEESEYFP TEEEEEEEDD EVEGAEADLS GDGT DYELK PLPKGGKRQK KVPVQEIDDD FFPSSGEEAE AASVGEGGGG GRKVGRYRDD GDEDYYKQRL RRWNKLRLQD KEKRL KLED DSEESDAEFD EGFKVPGFLF KKLFKYQQTG VRWLWELHCQ QAGGILGDEM GLGKTIQIIA FLAGLSYSKI RTRGSN YRF EGLGPTVIVC PTTVMHQWVK EFHTWWPPFR VAILHETGSY THKKEKLIRD VAHCHGILIT SYSYIRLMQD DISRYDW HY VILDEGHKIR NPNAAVTLAC KQFRTPHRII LSGSPMQNNL RELWSLFDFI FPGKLGTLPV FMEQFSVPIT MGGYSNAS P VQVKTAYKCA CVLRDTINPY LLRRMKSDVK MSLSLPDKNE QVLFCRLTDE QHKVYQNFVD SKEVYRILNG EMQIFSGLI ALRKICNHPD LFSGGPKNLK GLPDDELEED QFGYWKRSGK MIVVESLLKI WHKQGQRVLL FSQSRQMLDI LEVFLRAQKY TYLKMDGTT TIASRQPLIT RYNEDTSIFV FLLTTRVGGL GVNLTGANRV VIYDPDWNPS TDTQARERAW RIGQKKQVTV Y RLLTAGTI EEKIYHRQIF KQFLTNRVLK DPKQRRFFKS NDLYELFTLT SPDASQSTET SAIFAGTGSD VQTPKCHLKR RI QPAFGAD HDVPKRKKFP ASNISVNDAT SSEEKSEAKG AEVNAVTSNR SDPLKDDPHM SSNVTSNDRL GEETNAVSGP EEL SVISGN GECSNSSGTG KTSMPSGDES IDEKLGLSYK RERPSQAQTE AFWENKQMEN NFYKHKSKTK HHSVAEEETL EKHL RPKQK PKNSKHCRDA KFEGTRIPHL VKKRRYQKQD SENKSEAKEQ SNDDYVLEKL FKKSVGVHSV MKHDAIMDGA SPDYV LVEA EANRVAQDAL KALRLSRQRC LGAVSGVPTW TGHRGISGAP AGKKSRFGKK RNSNFSVQHP SSTSPTEKCQ DGIMKK EGK DNVPEHFSGR AEDADSSSGP LASSSLLAKM RARNHLILPE RLESESGHLQ EASALLPTTE HDDLLVEMRN FIAFQAH TD GQASTREILQ EFESKLSASQ SCVFRELLRN LCTFHRTSGG EGIWKLKPEY C

UniProtKB: DNA excision repair protein ERCC-6

+
Macromolecule #18: CSB element

MacromoleculeName: CSB element / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.996685 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

+
Macromolecule #19: UV-stimulated scaffold protein A

MacromoleculeName: UV-stimulated scaffold protein A / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.72168 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDQKLSKLVE ELTTSGEPRL NPEKMKELKK ICKSSEEQLS RAYRLLIAQL TQEHAEIRLS AFQIVEELFV RSHQFRMLVV SNFQEFLEL TLGTDPAQPL PPPREAAQRL RQATTRAVEG WNEKFGEAYK KLALGYHFLR HNKKVDFQDT NARSLAERKR E EEKQKHLD ...String:
MDQKLSKLVE ELTTSGEPRL NPEKMKELKK ICKSSEEQLS RAYRLLIAQL TQEHAEIRLS AFQIVEELFV RSHQFRMLVV SNFQEFLEL TLGTDPAQPL PPPREAAQRL RQATTRAVEG WNEKFGEAYK KLALGYHFLR HNKKVDFQDT NARSLAERKR E EEKQKHLD KIYQERASQA EREMQEMSGE IESCLTEVES CFRLLVPFDF DPNPETESLG MASGMSDALR SSCAGQVGPC RS GTPDPRD GEQPCCSRDL PASAGHPRAG GGAQPSQTAT GDPSDEDEDS DLEEFVRSHG LGSHKYTLDV ELCSEGLKVQ ENE DNLALI HAARDTLKLI RNKFLPAVCS WIQRFTRVGT HGGCLKRAID LKAELELVLR KYKELDIEPE GGERRRTEAL GDAE EDEDD EDFVEVPEKE GYEPHIPDHL RPEYGLEAAP EKDTVVRCLR TRTRMDEEVS DPTSAAAQLR QLRDHLPPPS SASPS RALP EPQEAQKLAA ERARAPVVPY GVDLHYWGQE LPTAGKIVKS DSQHRFWKPS EVEEEVVNAD ISEMLRSRHI TFAGKF EPV QHWCRAPRPD GRLCERQDRL KCPFHGKIVP RDDEGRPLDP EDRAREQRRQ LQKQERPEWQ DPELMRDVEA ATGQDLG SS RYSGKGRGKK RRYPSLTNLK AQADTARARI GRKVFAKAAV RRVVAAMNRM DQKKHEKFSN QFNYALN

UniProtKB: UV-stimulated scaffold protein A

+
Macromolecule #20: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.369719 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAMSYNYVV TAQKPTAVNG CVTGHFTSAE DLNLLIAKNT RLEIYVVTAE GLRPVKEVGM YGKIAVMELF RPKGESKDLL FILTAKYNA CILEYKQSGE SIDIITRAHG NVQDRIGRPS ETGIIGIIDP ECRMIGLRLY DGLFKVIPLD RDNKELKAFN I RLEELHVI ...String:
SNAMSYNYVV TAQKPTAVNG CVTGHFTSAE DLNLLIAKNT RLEIYVVTAE GLRPVKEVGM YGKIAVMELF RPKGESKDLL FILTAKYNA CILEYKQSGE SIDIITRAHG NVQDRIGRPS ETGIIGIIDP ECRMIGLRLY DGLFKVIPLD RDNKELKAFN I RLEELHVI DVKFLYGCQA PTICFVYQDP QGRHVKTYEV SLREKEFNKG PWKQENVEAE ASMVIAVPEP FGGAIIIGQE SI TYHNGDK YLAIAPPIIK QSTIVCHNRV DPNGSRYLLG DMEGRLFMLL LEKEEQMDGT VTLKDLRVEL LGETSIAECL TYL DNGVVF VGSRLGDSQL VKLNVDSNEQ GSYVVAMETF TNLGPIVDMC VVDLERQGQG QLVTCSGAFK EGSLRIIRNG IGIH EHASI DLPGIKGLWP LRSDPNRETD DTLVLSFVGQ TRVLMLNGEE VEETELMGFV DDQQTFFCGN VAHQQLIQIT SASVR LVSQ EPKALVSEWK EPQAKNISVA SCNSSQVVVA VGRALYYLQI HPQELRQISH TEMEHEVACL DITPLGDSNG LSPLCA IGL WTDISARILK LPSFELLHKE MLGGEIIPRS ILMTTFESSH YLLCALGDGA LFYFGLNIET GLLSDRKKVT LGTQPTV LR TFRSLSTTNV FACSDRPTVI YSSNHKLVFS NVNLKEVNYM CPLNSDGYPD SLALANNSTL TIGTIDEIQK LHIRTVPL Y ESPRKICYQE VSQCFGVLSS RIEVQDTSGG TTALRPSAST QALSSSVSSS KLFSSSTAPH ETSFGEEVEV HNLLIIDQH TFEVLHAHQF LQNEYALSLV SCKLGKDPNT YFIVGTAMVY PEEAEPKQGR IVVFQYSDGK LQTVAEKEVK GAVYSMVEFN GKLLASINS TVRLYEWTTE KELRTECNHY NNIMALYLKT KGDFILVGDL MRSVLLLAYK PMEGNFEEIA RDFNPNWMSA V EILDDDNF LGAENAFNLF VCQKDSAATT DEERQHLQEV GLFHLGEFVN VFCHGSLVMQ NLGETSTPTQ GSVLFGTVNG MI GLVTSLS ESWYNLLLDM QNRLNKVIKS VGKIEHSFWR SFHTERKTEP ATGFIDGDLI ESFLDISRPK MQEVVANLQY DDG SGMKRE ATADDLIKVV EELTRIH

UniProtKB: DNA damage-binding protein 1

+
Macromolecule #13: NTS

MacromoleculeName: NTS / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.494314 KDa
SequenceString:
(DC)(DT)(DA)(DG)(DT)(DT)(DG)(DA)(DT)(DC) (DT)(DC)(DA)(DT)(DA)(DT)(DT)(DT)(DC)(DA) (DT)(DT)(DC)(DC)(DT)(DA)(DC)(DT)(DC) (DA)(DG)(DG)(DA)(DG)(DA)(DA)(DG)(DG)(DA) (DG) (DC)(DA)(DG)(DA)(DG)(DC)(DG)

+
Macromolecule #14: TS

MacromoleculeName: TS / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.269129 KDa
SequenceString:
(DC)(DG)(DC)(DT)(DC)(DT)(DG)(DC)(DT)(DC) (DC)(DT)(DT)(DC)(DT)(DC)(DC)(DC)(DA)(DT) (DC)(DC)(DT)(DC)(DT)(DC)(DG)(DA)(DT) (DG)(DG)(DC)(DT)(DA)(DT)(DG)(DA)(DG)(DA) (DT) (DC)(DA)(DA)(DC)(DT)(DA)(DG)

+
Macromolecule #15: RNA

MacromoleculeName: RNA / type: rna / ID: 15 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.264036 KDa
SequenceString:
AUCGAGAGGA

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Macromolecule #21: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 21 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #22: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 22 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 10300 / Average electron dose: 40.4 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

+
Image processing

Particle selectionNumber selected: 2527839
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Number of particles is different for every focused refined map, as detailed in the manuscript.
Number images used: 100000
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
FSC plot (resolution estimation)

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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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