3KDF: Replication protein A 14 kDa subunit

Name: PDB 3KDF: X-ray Crystal Structure of the Human Replication Protein A Complex from Wheat Germ Cell Free Expression
Published: 2009-12-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: replication

X-ray Crystal Structure of the Human Replication Protein A Complex from Wheat Germ Cell Free Expression. Determined by X-ray diffraction at 1.98 Å resolution. Released 1 Dec 2009.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,185
Mol. weight: 57.95 kDa
Released: 1 Dec 2009

Explore 3KDF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KDF contains 17 α-helices and 30 β-strands across 4 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, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	10-12	3	1
α-helix	14-20	7
β-strand	24-34	11	1
β-strand	40-44	5	1
β-strand	50-54	5	1
β-strand	66-73	8	1
β-strand	79-86	8	1
α-helix	87-88	2
α-helix	96-108	13
α-helix	110-112	3

Chain B: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	47-48	2	5
α-helix	51-56	6
β-strand	58-60	3	6
β-strand	63-66	4	6
β-strand	69-71	3	6
β-strand	73-85	13	5
β-strand	89-95	7	5
β-strand	102-107	6	5
α-helix	119-121	3
β-strand	125-135	11	5
β-strand	138-148	11	5
α-helix	153-169	17

Chain C: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	10-12	3	4
α-helix	14-16	3
α-helix	18-20	3
β-strand	24-34	11	4
β-strand	40-44	5	4
β-strand	50-54	5	4
β-strand	66-73	8	4
β-strand	79-86	8	4
α-helix	87-88	2
α-helix	96-108	13
α-helix	110-112	3

Chain D: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	47-48	2	2
α-helix	51-55	5
β-strand	58-59	2	3
β-strand	64-66	3	3
β-strand	69-70	2	3
β-strand	73-85	13	2
β-strand	89-95	7	2
β-strand	102-107	6	2
α-helix	119-121	3
β-strand	125-135	11	2
β-strand	138-148	11	2
α-helix	153-171	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Replication protein A 14 kDa subunit	A, C	protein	121	Homo sapiens	P35244 (AlphaFold model)
Replication protein A 32 kDa subunit	B, D	protein	132	Homo sapiens	P15927 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3KDF_1 Replication protein A 14 kDa subunit (chains A, C)
SVDMMDLPRSRINAGMLAQFIDKPVCFVGRLEKIHPTGKMFILSDGEGKNGTIELMEPLD
EEISGIVEVVGRVTAKATILCTSYVQFKEDSHPFDLGLYNEAVKIIHDFPQFYPLGIVQH
D

Sequence of entity 2 (B, D), FASTA

>3KDF_2 Replication protein A 32 kDa subunit (chains B, D)
SRAQHIVPCTISQLLSATLVDEVFRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAA
PMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHIL
EVINAHMVLSKA

Primary citation

X-ray Crystal Structure of the Human Replication Protein A Complex from Wheat Germ Cell Free Expression. Makino, S.-I., Burgie, E.S., Bingman, C.A. et al. To be published.

Other PDB entries of the same protein (UniProt P35244 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2PI2 2.0 Å, Full-length Replication protein A subunits RPA14 and RPA32
1QUQ 2.5 Å, Complex of replication protein A subunits RPA14 and RPA32
2PQA 2.5 Å, Crystal Structure of Full-length Human RPA 14/32 Heterodimer
1L1O 2.8 Å, Structure of the human Replication Protein A (RPA) trimerization core
2Z6K 3.0 Å, Crystal structure of full-length human RPA14/32 heterodimer
8RK2 3.2 Å, Human Replication protein A (RPA; trimeric core) - ssDNA complex
9PD3 3.3 Å, NER dual incision complex - DuIS
9PD4 3.4 Å, NER dual incision complex - DuIM
9MJ5 3.5 Å, Catalytic domain of human DNA polymerase alpha in complex with DNA and RPA
9A1V Integrative model of Nucleotide excision repair complex of XPA and RPA on 5' junction…
9A1Y Integrative model of Nucleotide excision repair complex of XPA and RPA on 3' junction…
9A88 Structure of the pre-incision complex in nucleotide excision repair

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