Structure of PDB 5w65 Chain B

Receptor sequence

>5w65B (length=1178) Species: 559292 (Saccharomyces cerevisiae S288C)

RTADFRTLERESRFINPPKDKSAFPLLQEAVQPHIGSFNALTEGPDGGLL
NLGVKDIGEKVIFDGKPLNSNSGYLGNKLSVSVEQVSIAKPMSNDGVSSA
VERKVYPSESRQRLTSYRGKLLLKLKWSVNNGEENLFEVRDCGGLPVMLQ
SNRCHLNKMSPYELVQHKEESDEIGGYFIVNGIEKLIRMLIVQRRNHPMA
IIRPSFANRGASYSHYGIQIRSVRPDQTSQTNVLHYLNDGQVTFRFSWRK
NEYLVPVVMILKALCHTSDREIFDGIIGNDVKDSFLTDRLELLLRGFKKR
YPHLQNRTQVLQYLGDKFRVVFQASPDQSDLEVGQEVLDRIVLVHLGKDG
SQDKFRMLLFMIRKLYSLVAGECSPDNPDATQHQEVLLGGFLYGMILKEK
IDEYLQNIIAQVRMDINRGMAINFKDKRYMSRVLMRVNENIGSKMQYFLS
TGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFRMVHRGSFFAQLKTTT
VRKLLPESWGFLCPVHTPDGSPCGLLNHFAHKCRISTQQSDVSRIPSILY
SLGVAPASHTFAAGPSLCCVQIDGKIIGWVSHEQGKIIADTLRYWKVEGK
TPGLPIDLEIGYVPPSTRGQYPGLYLFGGHSRMLRPVRYLPLDKEDIVGP
FEQVYMNIAVTPQEIQNNVHTHVEFTPTNILSILANLTPFSDFNQSPRNM
YQCQMGKQTMGTPGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFP
NGFNAVVAVISYTGYDMDDAMIINKSADERGFGYGTMYKTEKVDLALNRN
RGDPITQHFGFGNDEWPKEWLEKLDEDGLPYIGTYVEEGDPICAYFDDTL
NKTKIKTYHSSEPAYIEEVNLIGDESNKFQELQTVSIKYRIRRTPQIGDK
FSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTIGMFVES
LAGKAGALHGIAQDSTPWIFNEDDTPADYFGEQLAKAGYNYHGNEPMYSG
ATGEELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRH
GGIRVGEMERDALIGHGTSFLLQDRLLNSSDYTQASVCRECGSILTTQQS
VPRIGSISTVCCRRCSMRFEDAKKLLTEDGEKIFIDDSQIWEDGQGNKFV
GGNETTTVAIPFVLKYLDSELSAMGIRL

3D structure

• PDB: 5w65 Structural mechanism of ATP-independent transcription initiation by RNA polymerase I.
• Chain: B
• Resolution: 4.3 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.6: DNA-directed RNA polymerase.

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	B	R495 Q724 K916 K924 H1038	R479 Q708 K900 K908 H1022
BS02	dna	B	R219 S221 R261 E268 L478 Q479 F508 K513 R815 N816 R817	R203 S205 R245 E252 L462 Q463 F492 K497 R799 N800 R801
BS03	dna	B	V113 S114 S115 E419 M430 K460 Y463 G1062 R1063 R1065 I1069 R1070 G1072	V97 S98 S99 E403 M414 K444 Y447 G1046 R1047 R1049 I1053 R1054 G1056
BS04	ZN	B	C1104 C1107 C1131	C1088 C1091 C1115

Gene Ontology

Molecular Function

• GO:0001054 RNA polymerase I activity
• GO:0003677 DNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016779 nucleotidyltransferase activity
• GO:0032549 ribonucleoside binding
• GO:0034062 5'-3' RNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006351 DNA-templated transcription
• GO:0006360 transcription by RNA polymerase I
• GO:0006361 transcription initiation at RNA polymerase I promoter
• GO:0006362 transcription elongation by RNA polymerase I
• GO:0006363 termination of RNA polymerase I transcription
• GO:0042254 ribosome biogenesis
• GO:0042790 nucleolar large rRNA transcription by RNA polymerase I

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex
• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005736 RNA polymerase I complex

External links

• PDB: RCSB:5w65, PDBe:5w65, PDBj:5w65
• PDBsum: 5w65
• PubMed: 28623663
• UniProt: P22138|RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135 (Gene Name=RPA135)