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NMR Structure - model 1 (Jmol Viewer)

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Title :   HUMAN REPLICATION PROTEIN A: GLOBAL FOLD OF THE N-TERMINAL RPA-70 DOMAIN REVEALS A BASIC CLEFT AND FLEXIBLE C-TERMINAL LINKER

Authors :   D. M. Jacobs, A. S. Lipton, N. G. Isern, G. W. Daughdrill, D. F. Lowry, X. Gomes, M. S. Wold

Date :   25 Apr 00 (Deposition) - 10 May 00 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A

Keywords :   5-Stranded Anti-Parallel, Beta Barrel, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. M. Jacobs, A. S. Lipton, N. G. Isern, G. W. Daughdrill, D. F. Lowry, X. Gomes, M. S. Wold
Human Replication Protein A: Global Fold Of The N-Terminal Rpa-70 Domain Reveals A Basic Cleft And Flexible C-Terminal Linker.
J. Biomol. Nmr V. 14 321 1999
PubMed-ID: 10526407 | Reference-DOI: 10.1023/A:1008373009786
(for further references see the PDB file header)

Molecule 1 - REPLICATION PROTEIN A
	Chains	:	A
	Fragment	:	N-TERMINAL FRAGMENT (RESIDUES 1-114)
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RPA70


NMR Structure	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1EWI)

(no "Site" information available for 1EWI)

(no "SS Bond" information available for 1EWI)

(no "Cis Peptide Bond" information available for 1EWI)

(no "SAP(SNP)/Variant" information available for 1EWI)

(no "PROSITE Motif" information available for 1EWI)

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000254719	1	ENSE00001236253	chr17:1733266-1733420	155	RFA1_HUMAN	1-11	11	1	A:1-11	11
1.2	ENST00000254719	2	ENSE00001236273	chr17:1746097-1746147	51	RFA1_HUMAN	12-28	17	1	A:12-28	17
1.3	ENST00000254719	3	ENSE00001236246	chr17:1747214-1747292	79	RFA1_HUMAN	29-55	27	1	A:29-55	27
1.4	ENST00000254719	4	ENSE00001236240	chr17:1747872-1747980	109	RFA1_HUMAN	55-91	37	1	A:55-91	37
1.5	ENST00000254719	5	ENSE00001236237	chr17:1756395-1756483	89	RFA1_HUMAN	91-121	31	1	A:91-114	24
1.6	ENST00000254719	6	ENSE00001198002	chr17:1775728-1775820	93	RFA1_HUMAN	121-152	32	0	-	-
1.7	ENST00000254719	7	ENSE00001197997	chr17:1778955-1779087	133	RFA1_HUMAN	152-196	45	0	-	-
1.8	ENST00000254719	8	ENSE00000904194	chr17:1780506-1780608	103	RFA1_HUMAN	196-230	35	0	-	-
1.9	ENST00000254719	9	ENSE00000904193	chr17:1782287-1782355	69	RFA1_HUMAN	231-253	23	0	-	-
1.10	ENST00000254719	10	ENSE00000904192	chr17:1782509-1782701	193	RFA1_HUMAN	254-318	65	0	-	-
1.11	ENST00000254719	11	ENSE00001310575	chr17:1782854-1782993	140	RFA1_HUMAN	318-364	47	0	-	-
1.12	ENST00000254719	12	ENSE00001197976	chr17:1783837-1783985	149	RFA1_HUMAN	365-414	50	0	-	-
1.13	ENST00000254719	13	ENSE00001132340	chr17:1787106-1787238	133	RFA1_HUMAN	414-458	45	0	-	-
1.14	ENST00000254719	14	ENSE00001116065	chr17:1791969-1792145	177	RFA1_HUMAN	459-517	59	0	-	-
1.15	ENST00000254719	15	ENSE00001116060	chr17:1795127-1795234	108	RFA1_HUMAN	518-553	36	0	-	-
1.16	ENST00000254719	16	ENSE00001116063	chr17:1798303-1798389	87	RFA1_HUMAN	554-582	29	0	-	-
1.17	ENST00000254719	17	ENSE00001236266	chr17:1800365-1802848	2484	RFA1_HUMAN	583-616	34	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:114
 aligned with RFA1_HUMAN | P27694 from UniProtKB/Swiss-Prot  Length:616

    Alignment length:114
                                    10        20        30        40        50        60        70        80        90       100       110    
           RFA1_HUMAN     1 MVGQLSEGAIAAIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNPLVEEEQLSSNCVCQIHRFIVNTLKDGRRVVILMELEVLKSAEAVGVKIGN 114
               SCOP domains d1ewia_ A: Replication protein A 70 KDa subunit (RPA70)                                                            SCOP domains
               CATH domains 1ewiA00 A:1-114 Nucleic acid-binding proteins                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhh.........eeeeeeeee.......eeeeeee...........hhhhh.hhhhhh.....ee....eeee.......eeee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1   Exon 1.2         Exon 1.3  PDB: A:29-55     -----------------------------------Exon 1.5  PDB: A:91-114  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.4  PDB: A:55-91 UniProt: 55-91----------------------- Transcript 1 (2)
                 1ewi A   1 MVGQLSEGAIAAIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNPLVEEEQLSSNCVCQIHRFIVNTLKDGRRVVILMELEVLKSAEAVGVKIGN 114
                                    10        20        30        40        50        60        70        80        90       100       110

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( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: OB-fold (1179)

Superfamily: Nucleic acid-binding proteins (590)

Family: Single strand DNA-binding domain, SSB (96)

Protein domain: Replication protein A 70 KDa subunit (RPA70) (4)

Human (Homo sapiens) [TaxId: 9606] (4)

d1ewia_

NMR Structure

Classes(

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Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: Nucleic acid-binding proteins (483)

Human (Homo sapiens) (27)

1ewiA00

A:1-114

(no "Pfam Domain" information available for 1EWI)

NMR Structure(hide GO term definitions)

Chain A (RFA1_HUMAN | P27694)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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.
biological process
	GO:0042769	DNA damage response, detection of DNA damage	The series of events required to receive a stimulus indicating DNA damage has occurred and convert it to a molecular signal.
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	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:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006261	DNA-dependent DNA replication	A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
	GO:0000082	G1/S transition of mitotic cell cycle	The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
	GO:0006284	base-excision repair	In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
	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: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:0070987	error-free translesion synthesis	The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions but does not causes an increase in the endogenous mutation level. For S. cerevisiae, RAD30 encodes DNA polymerase eta, which incorporates two adenines. When incorporated across a thymine-thymine dimer, it does not increase the endogenous mutation level.
	GO:0042276	error-prone translesion synthesis	The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions and causes an increase in the endogenous mutation level. For example, in E. coli, a low fidelity DNA polymerase, pol V, copies lesions that block replication fork progress. This produces mutations specifically targeted to DNA template damage sites, but it can also produce mutations at undamaged sites.
	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:0006298	mismatch repair	A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
	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:0006297	nucleotide-excision repair, DNA gap filling	Repair of the gap in the DNA helix by DNA polymerase and DNA ligase after the portion of the strand containing the lesion has been removed by pyrimidine-dimer repair enzymes.
	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:0006294	nucleotide-excision repair, preincision complex assembly	The aggregation, arrangement and bonding together of proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA 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:0016925	protein sumoylation	The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
	GO:1900034	regulation of cellular response to heat	Any process that modulates the frequency, rate or extent of cellular response to heat.
	GO:1901796	regulation of signal transduction by p53 class mediator	Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
	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:0000722	telomere maintenance via recombination	Any recombinational process that contributes to the maintenance of proper telomeric length.
	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.
	GO:0019985	translesion synthesis	The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.
cellular component
	GO:0005662	DNA replication factor A complex	A conserved heterotrimeric complex that binds nonspecifically to single-stranded DNA and is required for multiple processes in eukaryotic DNA metabolism, including DNA replication, DNA repair, and recombination. In all eukaryotic organisms examined the complex is composed of subunits of approximately 70, 30, and 14 kDa.
	GO:0016605	PML body	A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
	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: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.

NMR Structure
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Exons (5, 5)

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