SCOPe 2.08: Structural Classification of Proteins

PDB entry 1y77

View 1y77 on RCSB PDB site
Description: Complete RNA Polymerase II elongation complex with substrate analogue GMPCPP
Class: transcription,transferase/DNA-RNA hybrid
Keywords: Transcription, substrate, NTP, elongation, TRANSCRIPTION,TRANSFERASE-DNA-RNA HYBRID COMPLEX
Deposited on 2004-12-08, released 2005-01-04
The last revision prior to the SCOPe 2.08 freeze date was dated 2012-04-18, with a file datestamp of 2012-04-13.
Experiment type: XRAY
Resolution: 4.5 Å
R-factor: 0.297
AEROSPACI score: -0.01 (click here for full SPACI score report)

Chains and heterogens:

Chain 'A':
Compound: DNA-directed RNA polymerase II largest subunit
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P04050
Domains in SCOPe 2.08: d1y77a_
Chain 'B':
Compound: DNA-directed RNA polymerase II 140 kDa polypeptide
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P08518 (Start-1223)
Domains in SCOPe 2.08: d1y77b_
Chain 'C':
Compound: DNA-directed RNA polymerase II 45 kDa polypeptide
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P16370
Domains in SCOPe 2.08: d1y77c_
Chain 'D':
Compound: DNA-directed RNA polymerase II 32 kDa polypeptide
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P20433 (Start-220)
Domains in SCOPe 2.08: d1y77d_
Chain 'E':
Compound: DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P20434 (Start-214)
Domains in SCOPe 2.08: d1y77e_
Chain 'F':
Compound: DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P20435 (Start-154)
Domains in SCOPe 2.08: d1y77f_
Chain 'G':
Compound: DNA-directed RNA polymerase II 19 kDa polypeptide
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P34087 (0-170)
Domains in SCOPe 2.08: d1y77g_
Chain 'H':
Compound: DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P20436 (Start-145)
Domains in SCOPe 2.08: d1y77h_
Chain 'I':
Compound: DNA-directed RNA polymerase II subunit 9
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P27999
Domains in SCOPe 2.08: d1y77i_
Chain 'J':
Compound: DNA-directed RNA polymerases I/II/III subunit 10
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P22139 (0-End)
Domains in SCOPe 2.08: d1y77j_
Chain 'K':
Compound: DNA-directed RNA polymerase II 13.6 kDa polypeptide
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P38902 (0-End)
Domains in SCOPe 2.08: d1y77k_
Chain 'L':
Compound: DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
Species: Saccharomyces cerevisiae [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P40422 (Start-69)
Domains in SCOPe 2.08: d1y77l_
Chain 'N':
Compound: 5'-d(*ap*ap*gp*tp*ap*cp*t)-3'
Species: synthetic, synthetic
Chain 'P':
Compound: 5'-r(*ap*ap*gp*ap*cp*cp*ap*gp*gp*c)-3'
Species: synthetic, synthetic
Chain 'T':
Compound: 5'-d(p*ap*gp*tp*ap*cp*tp*tp*ap*cp*t*cp*gp*cp*cp*tp*gp*gp*tp*cp*tp*g)-3'
Species: synthetic, synthetic
Heterogens: ZN, MG, G2P

PDB Chain Sequences:

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

>1y77A (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