2ZJB - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HUMAN DMC1-M200V POLYMORPHIC VARIANT

Authors :   J. Hikiba, K. Hirota, W. Kagawa, S. Ikawa, T. Kinebuchi, I. Sakane, Y. Takizawa, S. Yokoyama, B. Mandon-Pepin, A. Nicolas, T. Shibata, K. Ohta, H. Kurumizaka

Date :   02 Mar 08 (Deposition) - 12 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)

Keywords :   Dna-Binding Protein, Ring Protein, Octamer, Aaa Atpase, Atp- Binding, Cell Cycle, Meiosis, Nucleotide-Binding, Nucleus, Polymorphism, Recombination (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Hikiba, K. Hirota, W. Kagawa, S. Ikawa, T. Kinebuchi, I. Sakane, Y. Takizawa, S. Yokoyama, B. Mandon-Pepin, A. Nicolas, T. Shibata, K. Ohta, H. Kurumizaka
Structural And Functional Analyses Of The Dmc1-M200V Polymorphism Found In The Human Population
Nucleic Acids Res. V. 36 4181 2008
PubMed-ID: 18566005 | Reference-DOI: 10.1093/NAR/GKN362
(for further references see the PDB file header)

Molecule 1 - MEIOTIC RECOMBINATION PROTEIN DMC1/LIM15 HOMOLOG
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DMC1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A	B

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2ZJB)

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

Asymmetric Unit

No.	Residues
1	Asp A:223	-	Ser A:224
2	Asp B:223	-	Ser B:224

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_061757	G	150	D	DMC1_HUMAN	Polymorphism	58396845	A/B	G	150	D
2	UniProt	VAR_018960	M	200	V	DMC1_HUMAN	Polymorphism	2227914	A/B	V	200	V

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

Biological Unit 1 (2, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_061757	G	150	D	DMC1_HUMAN	Polymorphism	58396845	A/B	G	150	D
2	UniProt	VAR_018960	M	200	V	DMC1_HUMAN	Polymorphism	2227914	A/B	V	200	V

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECA_2	PS50162	RecA family profile 1.	DMC1_HUMAN	97-270	2	A:97-270 B:97-270
2	RECA_3	PS50163	RecA family profile 2.	DMC1_HUMAN	277-340	2	A:290-340 B:290-340

Biological Unit 1 (2, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECA_2	PS50162	RecA family profile 1.	DMC1_HUMAN	97-270	8	A:97-270 B:97-270
2	RECA_3	PS50163	RecA family profile 2.	DMC1_HUMAN	277-340	8	A:290-340 B:290-340

Asymmetric Unit (10, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000216024	1a	ENSE00001948236	chr22:38966291-38966048	244	DMC1_HUMAN	-	0	0	-	-
1.3b	ENST00000216024	3b	ENSE00002166141	chr22:38964294-38964211	84	DMC1_HUMAN	1-17	17	0	-	-
1.4	ENST00000216024	4	ENSE00000880297	chr22:38963632-38963588	45	DMC1_HUMAN	18-32	15	0	-	-
1.5	ENST00000216024	5	ENSE00000654388	chr22:38962741-38962595	147	DMC1_HUMAN	33-81	49	0	-	-
1.6	ENST00000216024	6	ENSE00000654385	chr22:38958374-38958292	83	DMC1_HUMAN	82-109	28	2	A:83-109 B:83-109	27 27
1.7	ENST00000216024	7	ENSE00000654384	chr22:38951414-38951362	53	DMC1_HUMAN	109-127	19	2	A:109-127 B:109-127	19 19
1.8b	ENST00000216024	8b	ENSE00000654383	chr22:38948712-38948671	42	DMC1_HUMAN	127-141	15	2	A:127-141 B:127-141	15 15
1.9a	ENST00000216024	9a	ENSE00000654382	chr22:38946002-38945930	73	DMC1_HUMAN	141-165	25	2	A:141-165 B:141-165	25 25
1.10	ENST00000216024	10	ENSE00000654381	chr22:38935417-38935326	92	DMC1_HUMAN	165-196	32	2	A:165-196 B:165-196	32 32
1.11	ENST00000216024	11	ENSE00000654379	chr22:38934617-38934544	74	DMC1_HUMAN	196-220	25	2	A:196-220 B:196-220	25 25
1.12	ENST00000216024	12	ENSE00002152839	chr22:38934414-38934300	115	DMC1_HUMAN	221-259	39	2	A:221-259 B:221-259	39 39
1.13	ENST00000216024	13	ENSE00000654377	chr22:38933657-38933597	61	DMC1_HUMAN	259-279	21	2	A:259-270 B:259-270	12 12
1.14	ENST00000216024	14	ENSE00000654376	chr22:38917729-38917613	117	DMC1_HUMAN	279-318	40	2	A:290-318 B:290-318	29 29
1.15b	ENST00000216024	15b	ENSE00001204821	chr22:38916094-38914954	1141	DMC1_HUMAN	318-340	23	2	A:318-340 B:318-340	23 23

Asymmetric Unit

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:239
 aligned with DMC1_HUMAN | Q14565 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:258
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        
           DMC1_HUMAN    83 PGFLTAFEYSEKRKMVFHITTGSQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADRFNVDHDAVLDNVLYARAYTSEHQMELLDYVAAKFHEEAGIFKLLIIDSIMALFRVDFSGRGELAERQQKLAQMLSRLQKISEEYNVAVFVTNQMTADPGATMTFQADPKKPIGGHILAHASTTRISLRKGRGELRIAKIYDSPEMPENEATFAITAGGIGDAKE 340
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2zjbA00 A:83-340 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh......hhhhhhhh........eeeee.....hhhhhhhhhhhhh...........eeeeee.....hhhhhhhhhhhh..hhhhhhhheeeee..hhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhh....hhhhhhhhhhhhhhhhhh.hhhhhh.....eeeee..-------------------.........eeeeeee....eeeeeeee........eeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------D-------------------------------------------------V-------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------RECA_2  PDB: A:97-270 UniProt: 97-270                                                                                                                                         ------RECA_3  PDB: A:290-340 UniProt: 277-340                          PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:83-109    -----------------Exon 1.8b      -----------------------Exon 1.10  PDB: A:165-196       ------------------------Exon 1.12  PDB: A:221-259              -------------------Exon 1.14  PDB: A:290-318 [INCOMPLETE]  ---------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.7           -------------Exon 1.9a  PDB: A:141-165------------------------------Exon 1.11  PDB: A:196-220--------------------------------------Exon 1.13            --------------------------------------Exon 1.15b              Transcript 1 (2)
                 2zjb A  83 PGFLTAFEYSEKRKMVFHITTGSQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADRFNVDHDAVLDNVLYARAYTSEHQVELLDYVAAKFHEEAGIFKLLIIDSIMALFRVDFSGRGELAERQQKLAQMLSRLQKISEEYNVAVFVTNQM-------------------GHILAHASTTRISLRKGRGELRIAKIYDSPEMPENEATFAITAGGIGDAKE 340
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       | -         -       292       302       312       322       332        
                                                                                                                                                                                                                     270                 290

Chain B from PDB  Type:PROTEIN  Length:239
 aligned with DMC1_HUMAN | Q14565 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:258
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        
           DMC1_HUMAN    83 PGFLTAFEYSEKRKMVFHITTGSQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADRFNVDHDAVLDNVLYARAYTSEHQMELLDYVAAKFHEEAGIFKLLIIDSIMALFRVDFSGRGELAERQQKLAQMLSRLQKISEEYNVAVFVTNQMTADPGATMTFQADPKKPIGGHILAHASTTRISLRKGRGELRIAKIYDSPEMPENEATFAITAGGIGDAKE 340
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2zjbB00 B:83-340 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                              CATH domains
           Pfam domains (1) Rad51-2zjbB01 B:83-339                                                                                                                                                                                                                                           - Pfam domains (1)
           Pfam domains (2) Rad51-2zjbB02 B:83-339                                                                                                                                                                                                                                           - Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhh...ee...hhhhhh.....ee...eeeee.....hhhhhhhhhhhhh...........eeeeee.....hhhhhhhhhhhhh.hhhhhh...eeee....hhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee..-------------------.hhhhhh..eeeeeee....eeeeee..........eeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------D-------------------------------------------------V-------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------RECA_2  PDB: B:97-270 UniProt: 97-270                                                                                                                                         ------RECA_3  PDB: B:290-340 UniProt: 277-340                          PROSITE
           Transcript 1 (1) Exon 1.6  PDB: B:83-109    -----------------Exon 1.8b      -----------------------Exon 1.10  PDB: B:165-196       ------------------------Exon 1.12  PDB: B:221-259              -------------------Exon 1.14  PDB: B:290-318 [INCOMPLETE]  ---------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.7           -------------Exon 1.9a  PDB: B:141-165------------------------------Exon 1.11  PDB: B:196-220--------------------------------------Exon 1.13            --------------------------------------Exon 1.15b              Transcript 1 (2)
                 2zjb B  83 PGFLTAFEYSEKRKMVFHITTGSQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADRFNVDHDAVLDNVLYARAYTSEHQVELLDYVAAKFHEEAGIFKLLIIDSIMALFRVDFSGRGELAERQQKLAQMLSRLQKISEEYNVAVFVTNQM-------------------GHILAHASTTRISLRKGRGELRIAKIYDSPEMPENEATFAITAGGIGDAKE 340
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       | -         -       292       302       312       322       332        
                                                                                                                                                                                                                     270                 290

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 '\|'

(no "SCOP Domain" information available for 2ZJB)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Human (Homo sapiens) (413)

1a	2zjbA00	A:83-340
1b	2zjbB00	B:83-340

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Rad51 (10)

Homo sapiens (Human) (3)

1a	Rad51-2zjbB01	B:83-339
1b	Rad51-2zjbB02	B:83-339

Asymmetric Unit(hide GO term definitions)

Chain A,B (DMC1_HUMAN | Q14565)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0008094	DNA-dependent ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0004520	endodeoxyribonuclease activity	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
	GO:0000400	four-way junction DNA binding	Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0000150	recombinase activity	Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA.
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
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:0000730	DNA recombinase assembly	The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA.
	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:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0070192	chromosome organization involved in meiotic cell cycle	A process of chromosome organization that is involved in a meiotic cell cycle.
	GO:0007292	female gamete generation	Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction.
	GO:0007276	gamete generation	The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell.
	GO:0007141	male meiosis I	A cell cycle process comprising the steps by which a cell progresses through male meiosis I, the first meiotic division in the male germline.
	GO:0051321	meiotic cell cycle	Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
	GO:0006312	mitotic recombination	The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles.
	GO:0001556	oocyte maturation	A developmental process, independent of morphogenetic (shape) change, that is required for an oocyte to attain its fully functional state. Oocyte maturation commences after reinitiation of meiosis commonly starting with germinal vesicle breakdown, and continues up to the second meiotic arrest prior to fertilization.
	GO:0001541	ovarian follicle development	The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure.
	GO:0007131	reciprocal meiotic recombination	The cell cycle process in which double strand breaks are formed and repaired through a double Holliday junction intermediate. This results in the equal exchange of genetic material between non-sister chromatids in a pair of homologous chromosomes. These reciprocal recombinant products ensure the proper segregation of homologous chromosomes during meiosis I and create genetic diversity.
	GO:0010212	response to ionizing radiation	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 a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.
	GO:0007286	spermatid development	The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
	GO:0042148	strand invasion	The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules.
	GO:0007129	synapsis	The meiotic cell cycle process where side by side pairing and physical juxtaposition of homologous chromosomes is created during meiotic prophase. Synapsis begins when the chromosome arms begin to pair from the clustered telomeres and ends when synaptonemal complex or linear element assembly is complete.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000781	chromosome, telomeric region	The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0000794	condensed nuclear chromosome	A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
	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.

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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Asp A:223 - Ser A:224	[ RasMol ]
		Asp B:223 - Ser B:224	[ RasMol ]

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	2zjb
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	DMC1_HUMAN \| Q14565	:	1v5w 4hyy

(no "Related Entries Specified in the PDB File" available for 2ZJB)

Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

PROSITE Motifs (2, 4)

Exons (10, 20)

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