6LAE: DNA-binding domain of human XPA

Crystal structure of the DNA-binding domain of human XPA in complex with DNA. Determined by X-ray diffraction at 2.81 Å resolution. Released 26 Feb 2020.

Method: X-ray diffraction
Resolution: 2.81 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,398
Mol. weight: 41.78 kDa
Ligands: ZN
Released: 26 Feb 2020

Explore 6LAE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6LAE contains 15 α-helices and 10 β-strands across 2 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: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	103-104	2	1
β-strand	111-112	2	1
α-helix	116-120	5
β-strand	138-140	3	2
α-helix	141-148	8
α-helix	152-156	5
α-helix	161-162	2
β-strand	165-167	3	2
α-helix	176-177	2
β-strand	178-182	5	2
α-helix	183-194	12
α-helix	198-215	18

Chain B: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	103-104	2	3
β-strand	111-112	2	3
α-helix	116-119	4
β-strand	138-140	3	4
α-helix	141-148	8
α-helix	152-156	5
α-helix	161-162	2
β-strand	164-167	4	4
α-helix	168-169	2
α-helix	176-177	2
β-strand	178-182	5	4
α-helix	183-194	12
α-helix	197-214	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA repair protein complementing XP-A cells	A, B	protein	145	Homo sapiens	P23025 (AlphaFold model)
DNA (5'-d(pgpcpaptpcptpcpgpcpcp*t)-3')	C	DNA	11	Homo sapiens
DNA (5'-d(ptpgpgpcpgpapgpaptpgp*c)-3')	D	DNA	11	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>6LAE_1 DNA repair protein complementing XP-A cells (chains A, B)
GSHMEFDYVICEECGKEFMDSYLMNHFDLPTCDNCRDADDKHKLITKTEAKQEYLLKDCD
LEKREPPLKFIVKKNPHHSQWGDMKLYLKLQIVKRSLEVWGSQEALEEAKEVRQENREKM
KQKKFDKKVKELRRAVRSSVWKRET

Sequence of entity 2 (C), FASTA

>6LAE_2 DNA (5'-D(P*GP*CP*AP*TP*CP*TP*CP*GP*CP*CP*T)-3') (chains C)
GCATCTCGCCT

Sequence of entity 3 (D), FASTA

>6LAE_3 DNA (5'-D(P*TP*GP*GP*CP*GP*AP*GP*AP*TP*GP*C)-3') (chains D)
TGGCGAGATGC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

New structural insights into the recognition of undamaged splayed-arm DNA with a single pair of non-complementary nucleotides by human nucleotide excision repair protein XPA. Lian, F.M., Yang, X., Jiang, Y.L. et al. Int J Biol Macromol (2020) 148:466-474. DOI 10.1016/j.ijbiomac.2020.01.169 · PubMed

Other PDB entries of the same protein (UniProt P23025 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6J44 2.06 Å, Crystal structure of the redefined DNA-binding domain of human XPA
9QEC 2.9 Å, Cryo-EM structure of the XPF-ERCC1-XPA complex
8EBU 3.3 Å, XPC release from Core7-XPA-DNA (Cy5)
9PD3 3.3 Å, NER dual incision complex - DuIS
9PD4 3.4 Å, NER dual incision complex - DuIM
6RO4 3.5 Å, Structure of the core TFIIH-XPA-DNA complex
7AD8 3.5 Å, Core TFIIH-XPA-DNA complex with modelled p62 subunit
9XYU 3.5 Å, NER complex - C7CAD.ATP
28KE 3.6 Å, Cryo-EM structure of the human holo-TFIIH-XPC-XPA complex bound to bulky lesion-mimic DNA
8EBX 3.6 Å, XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (AP)
8EBY 3.6 Å, XPC release from Core7-XPA-DNA (AP)
8EBT 3.9 Å, XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (Cy5)

Browse structure collections

About this viewer

MolViewer shows 6LAE directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.