8RK2: PDB entry 8RK2

Human Replication protein A (RPA; trimeric core) - ssDNA complex. Determined by electron microscopy at 3.2 Å resolution. Released 24 Apr 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,245
Mol. weight: 111.07 kDa
Released: 24 Apr 2024

Explore 8RK2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RK2 contains 10 α-helices and 27 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	442	1	1
α-helix	445-450	6
β-strand	460-471	12	1
β-strand	477	1	2
β-strand	480	1	3
β-strand	491-492	2	4
β-strand	498-500	3	4
β-strand	505-507	3	4
β-strand	511	1	3
β-strand	514	1	2
β-strand	516-521	6	1
β-strand	526-531	6	1
α-helix	533-540	8
α-helix	544-551	8
α-helix	555-565	11
β-strand	569-581	13	1
β-strand	584-595	12	1
α-helix	599-615	17

Chain B: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	58-60	3	5
β-strand	63-66	4	5
β-strand	69-70	2	5
β-strand	73-85	13	6
β-strand	89-95	7	6
β-strand	102-107	6	6
α-helix	120-121	2
β-strand	125-135	11	6
β-strand	138-148	11	6
α-helix	153-173	21

Chain C: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	10-12	3	7
α-helix	14-19	6
β-strand	24-34	11	7
β-strand	40-44	5	7
β-strand	50-54	5	7
β-strand	66-73	8	7
β-strand	79-86	8	7
α-helix	96-106	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Replication protein A 70 kDa DNA-binding subunit, N-terminally processed	A	protein	616	Homo sapiens	P27694 (AlphaFold model)
Replication protein A 32 kDa subunit	B	protein	270	Homo sapiens	P15927 (AlphaFold model)
Replication protein A 14 kDa subunit	C	protein	121	Homo sapiens	P35244 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8RK2_1 Replication protein A 70 kDa DNA-binding subunit, N-terminally processed (chains A)
MVGQLSEGAIAAIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLAT
QLNPLVEEEQLSSNCVCQIHRFIVNTLKDGRRVVILMELEVLKSAEAVGVKIGNPVPYNE
GLGQPQVAPPAPAASPAASSRPQPQNGSSGMGSTVSKAYGASKTFGKAAGPSLSHTSGGT
QSKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESGEIRATAFNE
QVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPCEDDHHLPTVQF
DFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTATL
WGEDADKFDGSRQPVLAIKGARVSDFGGRSLSVLSSSTIIANPDIPEAYKLRGWFDAEGQ
ALDGVSISDLKSGGVGGSNTNWKTLYEVKSENLGQGDKPDYFSSVATVVYLRKENCMYQA
CPTQDCNKKVIDQQNGLYRCEKCDTEFPNFKYRMILSVNIADFQENQWVTCFQESAEAIL
GQNAAYLGELKDKNEQAFEEVFQNANFRSFIFRVRVKVETYNDESRIKATVMDVKPVDYR
EYGRRLVMSIRRSALM

Sequence of entity 2 (B), FASTA

>8RK2_2 Replication protein A 32 kDa subunit (chains B)
MWNSGFESYGSSSYGGAGGYTQSPGGFGSPAPSQAEKKSRARAQHIVPCTISQLLSATLV
DEVFRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVV
PPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLSKANSQPSAGR
APISNPGMSEAGNFGGNSFMPANGLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVS
SIKQAVDFLSNEGHIYSTVDDDHFKSTDAE

Sequence of entity 3 (C), FASTA

>8RK2_3 Replication protein A 14 kDa subunit (chains C)
MVDMMDLPRSRINAGMLAQFIDKPVCFVGRLEKIHPTGKMFILSDGEGKNGTIELMEPLD
EEISGIVEVVGRVTAKATILCTSYVQFKEDSHPFDLGLYNEAVKIIHDFPQFYPLGIVQH
D

Primary citation

Mechanism of single-stranded DNA annealing by RAD52-RPA complex. Liang, C.C., Greenhough, L.A., Masino, L. et al. Nature (2024) 629:697-703. DOI 10.1038/s41586-024-07347-7 · PubMed

Other PDB entries of the same protein (UniProt P27694 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4O0A 1.2 Å, Fragment-Based Discovery of a Potent Inhibitor of Replication Protein A Protein-Protein…
5E7N 1.21 Å, Crystal Structure of RPA70N in complex with VU0085636
4IPC 1.22 Å, Structure of the N-terminal domain of RPA70, E7R mutant
4R4T 1.28 Å, Crystal Structure of RPA70N in complex with 5-(4-((4-(5-carboxyfuran-2-yl)phenylthioamido…
5N8A 1.28 Å, Structure of RPA70N in complex with PrimPol (fragment 480-560)
4R4O 1.33 Å, Crystal structure of RPA70N in complex with 5-(4-((4-(5-carboxyfuran-2-yl)benzyl)carbamot…
4NB3 1.35 Å, Crystal structure of RPA70N in complex with a 3,4 dichlorophenylalanine ATRIP derived…
4R4Q 1.35 Å, Crystal structure of RPA70N in complex with 5-(3-((N-(4-(5-carboxyfuran-2-yl)benzyl)aceta…
4LUV 1.4 Å, Fragment-Based Discovery of a Potent Inhibitor of Replication Protein A Protein-Protein…
4R4C 1.4 Å, Structure of RPA70N in complex with 5-(4-((4-(5-carboxyfuran-2-yl)-2-chlorobenzamido)meth…
4R4I 1.4 Å, Structure of RPA70N in complex with 5-(4-((6-(5-carboxyfuran-2-yl)-1-thioxo-3,4-dihydrois…
8K00 1.4 Å, RPA70N-MRE11 fusion

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