2KN7 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   STRUCTURE OF THE XPF-SINGLE STRAND DNA COMPLEX

Authors :   D. Das, G. E. Folkers, M. Van Dijk, N. G. J. Jaspers, J. H. J. Hoeijmakers R. Kaptein, R. Boelens

Date :   16 Aug 09 (Deposition) - 04 Aug 10 (Release) - 04 Jul 12 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B,C,D  (20x)
NMR Structure *: A,B,C,D  (1x)

Keywords :   Ner, Xpf/Ercc1, Hhh, Protein-Ssdna Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Das, G. E. Folkers, M. Van Dijk, N. G. J. Jaspers, J. H. J. Hoeijmakers, R. Kaptein, R. Boelens
The Structure Of The Xpf-Ssdna Complex Underscores The Distinct Roles Of The Xpf And Ercc1 Helix- Hairpin-Helix Domains In Ss/Ds Dna Recognition
Structure V. 20 667 2012
PubMed-ID: 22483113 | Reference-DOI: 10.1016/J.STR.2012.02.009

Molecule 1 - DNA REPAIR ENDONUCLEASE XPF
	Chains	:	A, D
	EC Number	:	3.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PET28B
	Expression System Vector Type	:	VECTOR
	Fragment	:	RESIDUES IN UNP 842-908
	Gene	:	XPF
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DNA EXCISION REPAIR PROTEIN ERCC-4, DNA REPAIR PROTEIN COMPLEMENTING XP-F CELLS, XERODERMA PIGMENTOSUM GROUP F-COMPLEMENTING PROTEIN

*Molecule 2 - DNA (5'-D(CPAPGPTPGPGPCPTPGPA)-3')*
	Chains	:	B, C
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
NMR Structure (20x)	:	A	B	C	D
NMR Structure * (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2KN7)

(no "Site" information available for 2KN7)

(no "SS Bond" information available for 2KN7)

(no "Cis Peptide Bond" information available for 2KN7)

NMR Structure (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_057479	A	860	D	XPF_HUMAN	Polymorphism	4986933	A D	A	28 128	D
2	UniProt	VAR_019201	I	873	V	XPF_HUMAN	Polymorphism	2020957	A D	I	41 141	V
3	UniProt	VAR_013408	E	875	G	XPF_HUMAN	Polymorphism	1800124	A D	E	43 143	G

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

NMR Structure * (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_057479	A	860	D	XPF_HUMAN	Polymorphism	4986933	A A/D	A	28 128	D
2	UniProt	VAR_019201	I	873	V	XPF_HUMAN	Polymorphism	2020957	A A/D	I	41 141	V
3	UniProt	VAR_013408	E	875	G	XPF_HUMAN	Polymorphism	1800124	A A/D	E	43 143	G

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2KN7)

NMR Structure (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000311895	1a	ENSE00001307513	chr16:14014014-14014229	216	XPF_HUMAN	1-69	69	0	-	-
1.2	ENST00000311895	2	ENSE00001203019	chr16:14015888-14016068	181	XPF_HUMAN	70-130	61	0	-	-
1.3	ENST00000311895	3	ENSE00001203014	chr16:14020418-14020613	196	XPF_HUMAN	130-195	66	0	-	-
1.4	ENST00000311895	4	ENSE00001203009	chr16:14021885-14022092	208	XPF_HUMAN	195-264	70	0	-	-
1.5	ENST00000311895	5	ENSE00001203003	chr16:14024567-14024747	181	XPF_HUMAN	265-325	61	0	-	-
1.6b	ENST00000311895	6b	ENSE00001202996	chr16:14026014-14026142	129	XPF_HUMAN	325-368	44	0	-	-
1.8	ENST00000311895	8	ENSE00001202989	chr16:14028049-14028159	111	XPF_HUMAN	368-405	38	0	-	-
1.9a	ENST00000311895	9a	ENSE00001504946	chr16:14029003-14029600	598	XPF_HUMAN	405-604	200	0	-	-
1.10b	ENST00000311895	10b	ENSE00001202976	chr16:14031623-14031715	93	XPF_HUMAN	604-635	32	0	-	-
1.12	ENST00000311895	12	ENSE00001202971	chr16:14038580-14038692	113	XPF_HUMAN	635-673	39	0	-	-
1.13c	ENST00000311895	13c	ENSE00001203025	chr16:14041471-14046205	4735	XPF_HUMAN	673-916	244	2	A:10-76 D:110-176	67 67

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:67
 aligned with XPF_HUMAN | Q92889 from UniProtKB/Swiss-Prot  Length:916

    Alignment length:67
                                   851       861       871       881       891       901       
            XPF_HUMAN   842 EKYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILGNAANAKQLYDFIHTSFAEV 908
               SCOP domains d2kn7a_ A: automated matches                                        SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.13c  PDB: A:10-76 UniProt: 673-916 [INCOMPLETE]              Transcript 1
                 2kn7 A  10 EKYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILGNAANAKQLYDFIHTSFAEV  76
                                    19        29        39        49        59        69

Chain B from PDB  Type:DNA  Length:10
                                          
                 2kn7 B   1 CAGTGGCTGA  10
                                    10

Chain C from PDB  Type:DNA  Length:10
                                          
                 2kn7 C   1 CAGTGGCTGA  10
                                    10

Chain D from PDB  Type:PROTEIN  Length:67
 aligned with XPF_HUMAN | Q92889 from UniProtKB/Swiss-Prot  Length:916

    Alignment length:67
                                   851       861       871       881       891       901       
            XPF_HUMAN   842 EKYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILGNAANAKQLYDFIHTSFAEV 908
               SCOP domains d2kn7d_ D: automated matches                                        SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------D------------V-G--------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.13c  PDB: D:110-176 UniProt: 673-916 [INCOMPLETE]            Transcript 1
                 2kn7 D 110 EKYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILGNAANAKQLYDFIHTSFAEV 176
                                   119       129       139       149       159       169

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

NMR Structure

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: SAM domain-like (639)

Superfamily: RuvA domain 2-like (26)

Family: Hef domain-like (9)

Protein domain: automated matches (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d2kn7a_	A:
1b	d2kn7d_	D:

(no "CATH Domain" information available for 2KN7)

(no "Pfam Domain" information available for 2KN7)

NMR Structure(hide GO term definitions)

Chain A,D (XPF_HUMAN | Q92889)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0001094	TFIID-class transcription factor binding	Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.
	GO:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	GO:0004520	endodeoxyribonuclease activity	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	GO:0047485	protein N-terminus binding	Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
	GO:0000014	single-stranded DNA endodeoxyribonuclease activity	Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks.
biological process
	GO:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0009650	UV protection	Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0034644	cellular response to UV	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
	GO:0000724	double-strand break repair via homologous recombination	The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.
	GO:0070911	global genome nucleotide-excision repair	The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
	GO:0036297	interstrand cross-link repair	Removal of a DNA interstrand crosslink (a covalent attachment of DNA bases on opposite strands of the DNA) and restoration of the DNA. DNA interstrand crosslinks occur when both strands of duplex DNA are covalently tethered together (e.g. by an exogenous or endogenous agent), thus preventing the strand unwinding necessary for essential DNA functions such as transcription and replication.
	GO:0032205	negative regulation of telomere maintenance	Any process that stops, prevents, or reduces the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.
	GO:0006289	nucleotide-excision repair	A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
	GO:1901255	nucleotide-excision repair involved in interstrand cross-link repair	Any nucleotide-excision repair that is involved in interstrand cross-link repair.
	GO:0033683	nucleotide-excision repair, DNA incision	A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.
	GO:0006295	nucleotide-excision repair, DNA incision, 3'-to lesion	The endonucleolytic cleavage of the damaged strand of DNA 3' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision precedes the incision formed 5' to the site of damage.
	GO:0006296	nucleotide-excision repair, DNA incision, 5'-to lesion	The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage.
	GO:0006293	nucleotide-excision repair, preincision complex stabilization	The stabilization of the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage as well as the unwound DNA. The stabilization of the protein-DNA complex ensures proper positioning of the preincision complex before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
	GO:0000712	resolution of meiotic recombination intermediates	The cleavage and rejoining of intermediates, such as Holliday junctions, formed during meiotic recombination to produce two intact molecules in which genetic material has been exchanged.
	GO:0009411	response to UV	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
	GO:0000723	telomere maintenance	Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
	GO:0006283	transcription-coupled nucleotide-excision repair	The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
cellular component
	GO:0070522	ERCC4-ERCC1 complex	A heterodimeric nucleotide-excision repair complex that has endonuclease activity specific for bubble structures characteristic of certain DNA lesions. The subunits are known as XPF/ERCC4 and ERCC1 in mammals, and Rad1p and Rad10p in S. cerevisiae.
	GO:0000781	chromosome, telomeric region	The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0000109	nucleotide-excision repair complex	Any complex formed of proteins that act in nucleotide-excision repair.
	GO:0000110	nucleotide-excision repair factor 1 complex	One of several protein complexes involved in nucleotide-excision repair; possesses DNA damage recognition and endodeoxynuclease activities. In S. cerevisiae, it is composed of Rad1p, Rad10p, and Rad14p; in human the subunits are ERCC4/XPF, ERCC1 and XPA, respectively.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005669	transcription factor TFIID complex	A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.

NMR Structure
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(no "Sites" information available for 2kn7)

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(no "Cis Peptide Bonds" information available for 2kn7)

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	2kn7
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	XPF_HUMAN \| Q92889
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	3.1.-.-
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	XPF_HUMAN \| Q92889	:	1z00 2a1j 2aq0 2mut

Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

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Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

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Exons (1, 2)

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