SCOPe 2.08: Structural Classification of Proteins

PDB entry 2ja5

View 2ja5 on RCSB PDB site
Description: CPD lesion containing RNA Polymerase II elongation complex A
Class: transferase
Keywords: DNA-directed RNA polymerase, lesion recognition, transferase/DNA/RNA, DNA damage, zinc-finger, DNA-binding, photolesion, phosphorylation, misincorporation, RNA polymerase II, transcription- coupled repair, cyclobutane pyrimidine dimer, tcr, cpd, zinc, arrest, stalling, DNA lesion, metal-binding, nuclear protein, transcription bubble, nucleotidyltransferase, damage recognition, elongation complex, transferase, thymine dimer, transcription
Deposited on 2006-11-23, released 2007-02-20
The last revision prior to the SCOPe 2.08 freeze date was dated 2017-03-29, with a file datestamp of 2017-03-24.
Experiment type: XRAY
Resolution: 3.8 Å
R-factor: N/A
AEROSPACI score: 0.05 (click here for full SPACI score report)

Chains and heterogens:

Chain 'A':
Compound: DNA-directed RNA polymerase II subunit RPB1
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P04050
Domains in SCOPe 2.08: d2ja5a1
Chain 'B':
Compound: DNA-directed RNA polymerase II subunit RPB2
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P08518 (Start-1223)
Domains in SCOPe 2.08: d2ja5b1
Chain 'C':
Compound: DNA-directed RNA polymerase II subunit RPB3
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P16370
Domains in SCOPe 2.08: d2ja5c1, d2ja5c2
Chain 'D':
Compound: DNA-directed RNA polymerase II subunit RPB4
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P20433 (Start-220)
Domains in SCOPe 2.08: d2ja5d1
Chain 'E':
Compound: DNA-directed RNA polymerases I, II, and III subunit RPABC1
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P20434 (Start-214)
Domains in SCOPe 2.08: d2ja5e1, d2ja5e2
Chain 'F':
Compound: DNA-directed RNA polymerases I, II, and III subunit RPABC2
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P20435 (Start-154)
Domains in SCOPe 2.08: d2ja5f1
Chain 'G':
Compound: DNA-directed RNA polymerase II subunit RPB7
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P34087 (0-170)
Domains in SCOPe 2.08: d2ja5g1, d2ja5g2
Chain 'H':
Compound: DNA-directed RNA polymerases I, II, and III subunit RPABC3
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P20436 (Start-145)
Domains in SCOPe 2.08: d2ja5h1
Chain 'I':
Compound: DNA-directed RNA polymerase II subunit RPB9
Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
Database cross-references and differences (RAF-indexed):
- Uniprot P27999
Domains in SCOPe 2.08: d2ja5i1, d2ja5i2
Chain 'J':
Compound: DNA-directed RNA polymerases I, II, and III subunit RPABC5
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P22139 (0-End)
Domains in SCOPe 2.08: d2ja5j1
Chain 'K':
Compound: DNA-directed RNA polymerase II subunit RPB11
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P38902 (0-End)
Domains in SCOPe 2.08: d2ja5k1
Chain 'L':
Compound: DNA-directed RNA polymerases I, II, and III subunit RPABC4
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P40422 (Start-69)
Domains in SCOPe 2.08: d2ja5l1
Chain 'P':
Compound: 5'-r(*up*up*cp*gp*ap*cp*cp*ap*gp*gp*ap)-3'
Species: synthetic construct, synthetic [TaxId:32630]
Chain 'T':
Compound: 5'-d(*ap*gp*cp*tp*cp*ap*ap*gp*tp*ap *cp*tp*ttp*tp*tp*cp*cp*brup*gp*gp*tp*cp*ap*tp*t)-3'
Species: synthetic construct, synthetic [TaxId:32630]
Heterogens: MG, ZN

PDB Chain Sequences:

Chain 'A':
Sequence, based on SEQRES records: (download)

>2ja5A (A:)
mvgqqyssaplrtvkevqfglfspeevraisvakirfpetmdetqtrakigglndprlgs
idrnlkcqtcqegmnecpghfghidlakpvfhvgfiakikkvcecvcmhcgkllldehne
lmrqalaikdskkrfaaiwtlcktkmvcetdvpseddptqlvsrggcgntqptirkdglk
lvgswkkdratgdadepelrvlsteeilnifkhisvkdftslgfnevfsrpewmiltclp
vppppvrpsisfnesqrgeddltfkladilkanisletlehngaphhaieeaesllqfhv
atymdndiagqpqalqksgrpvksirarlkgkegrirgnlmgkrvdfsartvisgdpnle
ldqvgvpksiaktltypevvtpynidrltqlvrngpnehpgakyvirdsgdridlryskr
agdiqlqygwkverhimdndpvlfnrqpslhkmsmmahrvkvipystfrlnlsvtspyna
dfdgdemnlhvpqseetraelsqlcavplqivspqsnkpcmgivqdtlcgirkltlrdtf
ieldqvlnmlywvpdwdgviptpaiikpkplwsgkqilsvaipngihlqrfdegttllsp
kdngmliidgqiifgvvekktvgssngglihvvtrekgpqvcaklfgniqkvvnfwllhn
gfstgigdtiadgptmreitetiaeakkkvldvtkeaqanlltakhgmtlresfednvvr
flneardkagrlaevnlkdlnnvkqmvmagskgsfiniaqmsacvgqqsvegkriafgfv
drtlphfskddyspeskgfvensylrgltpqefffhamggreglidtavktaetgyiqrr
lvkaledimvhydnttrnslgnviqfiygedgmdaahiekqsldtiggsdaafekryrvd
llntdhtldpsllesgseilgdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvni
rriiqnaqqtfhidhtkpsdltikdivlgvkdlqenllvlrgkneiiqnaqrdavtlfcc
llrsrlatrrvlqeyrltkqafdwvlsnieaqflrsvvhpgemvgvlaaqsigepatqmt
lntfhfagvaskkvtsgvprlkeilnvaknmktpsltvylepghaadqeqaklirsaieh
ttlksvtiaseiyydpdprstvipedeeiiqlhfslldeeaeqsfdqqspwllrleldra
amndkdltmgqvgerikqtfkndlfviwsedndekliircrvvrpksldaeteaeedhml
kkientmlenitlrgveniervvmmkydrkvpsptgeyvkepewvletdgvnlsevmtvp
gidptriytnsfidimevlgieagraalykevynviasdgsyvnyrhmallvdvmttqgg
ltsvtrhgfnrsntgalmrcsfeetveilfeagasaelddcrgvsenvilgqmapigtga
fdvmideeslvkympeqkiteiedgqdggvtpysnesglvnadldvkdelmfsplvdsgs
ndamaggftayggadygeatspfgaygeaptspgfgvsspgfsptsptysptspayspts
psysptspsysptspsysptspsysptspsysptspsysptspsysptspsysptspsys
ptspsysptspsysptspsysptspsysptspsysptspaysptspsysptspsysptsp
sysptspsysptspnysptspsysptspgyspgspayspkqdeqkhnenensr