Structure of PDB 8u9r Chain A

Receptor sequence

>8u9rA (length=1396) Species: 4932 (Saccharomyces cerevisiae)

GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGG
LNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKV
CECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDV
PSRGCGNTQPTIRKDGLKLVGSWKELRVLSTEEILNIFKHISVKDFTSLG
FNEVFSRPEWMILTCLPVPPPPVRPSISFQRGEDDLTFKLADILKANISL
ETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSPVKSIRAR
LKGKEGRRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEV
VTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYG
WKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYN
ADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLC
GIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILS
VAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGL
IHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREI
TETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKA
GRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGF
VDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAV
KTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIE
KQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLL
DEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPS
DLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATR
RVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQM
TLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQE
QAKLIRSAIEHTTLKSVTIASEIYYDPTVIPEDEEIIQLQQSPWLLRLEL
DRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVEEDH
MLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLET
DGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIAS
DGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEI
LFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYM

3D structure

• PDB: 8u9r Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser.
• Chain: A
• Resolution: 3.34 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	A	P448 D483 D485	P419 D454 D456
BS02	dna	A	K332 R337 R344 R350 Q447 T831 A832 G835 Y836 R839 R1386 E1403 E1404	K304 R308 R315 R321 Q418 T802 A803 G806 Y807 R810 R1328 E1345 E1346
BS03	ZN	A	C67 C70 C77 H80	C65 C68 C75 H78
BS04	MG	A	D481 D483 D485	D452 D454 D456
BS05	MG	A	D481 D483	D452 D454
BS06	ATP	A	R446 N479 D481 L1081 H1085	R417 N450 D452 L1052 H1056

External links

• PDB: RCSB:8u9r, PDBe:8u9r, PDBj:8u9r
• PDBsum: 8u9r
• PubMed: 39190355
• UniProt: P04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)