2QM4 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN XLF/CERNUNNOS, A NON-HOMOLOGOUS END-JOINING FACTOR

Authors :   Y. Li, D. Y. Chirgadze, B. L. Sibanda, V. M. Bolanos-Garcia, O. R. Davies T. L. Blundell

Date :   14 Jul 07 (Deposition) - 11 Dec 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Xrcc4 Like Factor, Homodimer, Beta-Sandwich, Coiled-Coil, Recombination (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Li, D. Y. Chirgadze, V. M. Bolanos-Garcia, B. L. Sibanda, O. R. Davies, P. Ahnesorg, S. P. Jackson, T. L. Blundell
Crystal Structure Of Human Xlf/Cernunnos Reveals Unexpected Differences From Xrcc4 With Implications For Nhej.
Embo J. V. 27 290 2008
PubMed-ID: 18046455 | Reference-DOI: 10.1038/SJ.EMBOJ.7601942

Molecule 1 - NON-HOMOLOGOUS END-JOINING FACTOR 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETG-41A
	Expression System Strain	:	ROSETTA2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NHEJ1, XLF
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN CERNUNNOS, XRCC4-LIKE FACTOR

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 36)

No.	Name	Count	Type	Full Name
1	MSE	36	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 18)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 18)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2QM4)

(no "SS Bond" information available for 2QM4)

(no "Cis Peptide Bond" information available for 2QM4)

Asymmetric Unit (4, 15)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_038790	A	14	T	NHEJ1_HUMAN	Polymorphism	34689457	A/B/C/D	A	14	T
2	UniProt	VAR_025704	R	57	G	NHEJ1_HUMAN	Disease (NHEJ1-SCID)	118204451	A/B/C/D	R	57	G
3	UniProt	VAR_038791	H	89	R	NHEJ1_HUMAN	Polymorphism	1056296	A/B/C	H	89	R
4	UniProt	VAR_025705	C	123	R	NHEJ1_HUMAN	Disease (NHEJ1-SCID)	118204452	A/B/C/D	C	123	R

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

Biological Unit 1 (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_038790	A	14	T	NHEJ1_HUMAN	Polymorphism	34689457	A/B	A	14	T
2	UniProt	VAR_025704	R	57	G	NHEJ1_HUMAN	Disease (NHEJ1-SCID)	118204451	A/B	R	57	G
3	UniProt	VAR_038791	H	89	R	NHEJ1_HUMAN	Polymorphism	1056296	A/B	H	89	R
4	UniProt	VAR_025705	C	123	R	NHEJ1_HUMAN	Disease (NHEJ1-SCID)	118204452	A/B	C	123	R

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

Biological Unit 2 (4, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_038790	A	14	T	NHEJ1_HUMAN	Polymorphism	34689457	C/D	A	14	T
2	UniProt	VAR_025704	R	57	G	NHEJ1_HUMAN	Disease (NHEJ1-SCID)	118204451	C/D	R	57	G
3	UniProt	VAR_038791	H	89	R	NHEJ1_HUMAN	Polymorphism	1056296	C	H	89	R
4	UniProt	VAR_025705	C	123	R	NHEJ1_HUMAN	Disease (NHEJ1-SCID)	118204452	C/D	C	123	R

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

(no "PROSITE Motif" information available for 2QM4)

Asymmetric Unit (5, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000356853	1b	ENSE00001869065	chr2:220025575-220025442	134	NHEJ1_HUMAN	-	0	0	-	-
1.4b	ENST00000356853	4b	ENSE00002167216	chr2:220023084-220022908	177	NHEJ1_HUMAN	1-59	59	4	A:1-59 B:1-59 C:1-59 D:1-59	59 59 59 59
1.5a	ENST00000356853	5a	ENSE00001708572	chr2:220022406-220022194	213	NHEJ1_HUMAN	60-130	71	4	A:60-130 B:60-130 C:60-130 D:60-130 (gaps)	71 71 71 71
1.6	ENST00000356853	6	ENSE00001664826	chr2:220012517-220012379	139	NHEJ1_HUMAN	131-177	47	4	A:131-177 B:131-177 (gaps) C:131-177 D:131-177	47 47 47 47
1.7b	ENST00000356853	7b	ENSE00001631569	chr2:220011460-220011402	59	NHEJ1_HUMAN	177-196	20	4	A:177-196 B:177-196 C:177-196 D:177-196	20 20 20 20
1.11b	ENST00000356853	11b	ENSE00001776599	chr2:219942928-219942811	118	NHEJ1_HUMAN	197-236	40	4	A:197-230 B:197-227 C:197-227 D:197-229	34 31 31 33
1.12	ENST00000356853	12	ENSE00001706214	chr2:219942086-219941968	119	NHEJ1_HUMAN	236-275	40	0	-	-
1.13f	ENST00000356853	13f	ENSE00001781266	chr2:219941177-219940043	1135	NHEJ1_HUMAN	276-299	24	0	-	-

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:232
 aligned with NHEJ1_HUMAN | Q9H9Q4 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:232
                              1                                                                                                                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228  
          NHEJ1_HUMAN     - --MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQEVQVGQ 230
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qm4A01 A:-1-141  [code=2.170.210.10, no name defined]                                                                                         -2qm4A02 A:143-230 Helix hairpin bin                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...eeee....eeeeeeeee..eeeeeee....eeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.......eeeeeee..eeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------T------------------------------------------G-------------------------------R---------------------------------R----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) --Exon 1.4b  PDB: A:1-59 UniProt: 1-59                       Exon 1.5a  PDB: A:60-130 UniProt: 60-130                               Exon 1.6  PDB: A:131-177 UniProt: 131-177      -------------------Exon 1.11b  PDB: A:197-230         Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7b           ---------------------------------- Transcript 1 (2)
                 2qm4 A  -1 SGmEELEQGLLmQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWNFHCmLASPSLVSQHLIRPLmGmSLALQCQVRELATLLHmKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFmIEKLPEACSIGDGKPFVmNLQDLYmAVTTQEVQVGQ 230
                              |      8 |      18        28        38        48        58        68        78        88        98       108       118     | 128       138 | |   148       158|      168       178       188     | 198       208   |   218|      228  
                              |       10-MSE                                                                                                           124-MSE         140-MSE            159-MSE                            194-MSE           212-MSE  |           
                              1-MSE                                                                                                                                      142-MSE                                                                      219-MSE

Chain B from PDB  Type:PROTEIN  Length:225
 aligned with NHEJ1_HUMAN | Q9H9Q4 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:229
                              1                                                                                                                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218         
          NHEJ1_HUMAN     - --MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQEVQ 227
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qm4B01 B:-1-141  [code=2.170.210.10, no name defined]                                                                                         -2qm4B02 B:143-227 Helix hai    rpin bin                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..eeee....eeeeeeeee..eeeeeee....eeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.......eeeeeee..eeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.----..hhhhh....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------T------------------------------------------G-------------------------------R---------------------------------R-------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) --Exon 1.4b  PDB: B:1-59 UniProt: 1-59                       Exon 1.5a  PDB: B:60-130 UniProt: 60-130                               Exon 1.6  PDB: B:131-177 (gaps)                -------------------Exon 1.11b  PDB: B:197-227      Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7b           ------------------------------- Transcript 1 (2)
                 2qm4 B  -1 SGmEELEQGLLmQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWNFHCmLASPSLVSQHLIRPLmGmSLALQCQVRELATLLHmKDLEIQDYQE----LIRDRLKTEPFEENSFLEQFmIEKLPEACSIGDGKPFVmNLQDLYmAVTTQEVQ 227
                              |      8 |      18        28        38        48        58        68        78        88        98       108       118     | 128       138 | |   148       158|      168|    | 178       188     | 198       208   |   218|        
                              1-MSE   10-MSE                                                                                                           124-MSE         140-MSE            159-MSE   169  174                 194-MSE           212-MSE  |        
                                                                                                                                                                         142-MSE                                                                      219-MSE

Chain C from PDB  Type:PROTEIN  Length:229
 aligned with NHEJ1_HUMAN | Q9H9Q4 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:229
                              1                                                                                                                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218         
          NHEJ1_HUMAN     - --MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQEVQ 227
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qm4C01 C:-1-141  [code=2.170.210.10, no name defined]                                                                                         -2qm4C02 C:143-227 Helix hairpin bin                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..eeee....eeeeeeeee..eeeeeee....eeeeeeehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.......eeeeeee..eeeeeeeee....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------T------------------------------------------G-------------------------------R---------------------------------R-------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) --Exon 1.4b  PDB: C:1-59 UniProt: 1-59                       Exon 1.5a  PDB: C:60-130 UniProt: 60-130                               Exon 1.6  PDB: C:131-177 UniProt: 131-177      -------------------Exon 1.11b  PDB: C:197-227      Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7b           ------------------------------- Transcript 1 (2)
                 2qm4 C  -1 SGmEELEQGLLmQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWNFHCmLASPSLVSQHLIRPLmGmSLALQCQVRELATLLHmKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFmIEKLPEACSIGDGKPFVmNLQDLYmAVTTQEVQ 227
                              |      8 |      18        28        38        48        58        68        78        88        98       108       118     | 128       138 | |   148       158|      168       178       188     | 198       208   |   218|        
                              1-MSE   10-MSE                                                                                                           124-MSE         140-MSE            159-MSE                            194-MSE           212-MSE  |        
                                                                                                                                                                         142-MSE                                                                      219-MSE

Chain D from PDB  Type:PROTEIN  Length:225
 aligned with NHEJ1_HUMAN | Q9H9Q4 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:231
                              1                                                                                                                                                                                                                                    
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228 
          NHEJ1_HUMAN     - --MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQEVQVG 229
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qm4D01 D:-1-141  [code=2.170.210.10, no name defined]                                                                                         -2qm4D02 D:143-229 Helix hairpin bin                                                     CATH domains
           Pfam domains (1) ------------XLF-2qm4D01 D:11-173                                                                                                                                               -------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------XLF-2qm4D02 D:11-173                                                                                                                                               -------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ------------XLF-2qm4D03 D:11-173                                                                                                                                               -------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ------------XLF-2qm4D04 D:11-173                                                                                                                                               -------------------------------------------------------- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhh...eeee....eeeeeeeee..eeeeeee....eeeeeeehhhhhhhhhhhh.....hhhhhhhhhhhhhh...------...eeeeeee..eeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------T------------------------------------------G-----------------------------------------------------------------R---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) --Exon 1.4b  PDB: D:1-59 UniProt: 1-59                       Exon 1.5a  PDB: D:60-130 (gaps) UniProt: 60-130                        Exon 1.6  PDB: D:131-177 UniProt: 131-177      -------------------Exon 1.11b  PDB: D:197-229        Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7b           --------------------------------- Transcript 1 (2)
                 2qm4 D  -1 SGmEELEQGLLmQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLL------SEATFSCDCVADALILRVRSELSGLPFYWNFHCmLASPSLVSQHLIRPLmGmSLALQCQVRELATLLHmKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFmIEKLPEACSIGDGKPFVmNLQDLYmAVTTQEVQVG 229
                              |      8 |      18        28        38        48        58        68        78     |   -  |     98       108       118     | 128       138 | |   148       158|      168       178       188     | 198       208   |   218|      228 
                              1-MSE   10-MSE                                                                    84     91                              124-MSE         140-MSE            159-MSE                            194-MSE           212-MSE  |          
                                                                                                                                                                         142-MSE                                                                      219-MSE

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 2QM4)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helix Hairpins (718)

Homologous Superfamily: Helix hairpin bin (4)

Human (Homo sapiens) (3)

1a	2qm4C02	C:143-227
1b	2qm4B02	B:143-227
1c	2qm4D02	D:143-229
1d	2qm4A02	A:143-230

Class: Mainly Beta (13760)

Architecture: Beta Complex (381)

Topology: Dna Repair Protein Xrcc4; Chain: A, domain 1 (5)

Homologous Superfamily: [code=2.170.210.10, no name defined] (5)

Human (Homo sapiens) (5)

2a	2qm4D01	D:-1-141
2b	2qm4A01	A:-1-141
2c	2qm4B01	B:-1-141
2d	2qm4C01	C:-1-141

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: XLF] (2)

Family: XLF (2)

Homo sapiens (Human) (2)

1a	XLF-2qm4D01	D:11-173
1b	XLF-2qm4D02	D:11-173
1c	XLF-2qm4D03	D:11-173
1d	XLF-2qm4D04	D:11-173

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (NHEJ1_HUMAN | Q9H9Q4)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic 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).
biological process
	GO:0030183	B cell differentiation	The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
	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:0030217	T cell differentiation	The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
	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:0007417	central nervous system development	The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
	GO:0006302	double-strand break repair	The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
	GO:0006303	double-strand break repair via nonhomologous end joining	The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
	GO:0051351	positive regulation of ligase activity	Any process that activates or increases the frequency, rate or extent of ligase activity, the catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate.
	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.
cellular component
	GO:0070419	nonhomologous end joining complex	A protein complex that plays a role in DNA double-strand break repair via nonhomologous end joining. Such complexes typically contain a specialized DNA ligase (e.g. Lig4 in eukaryotes) and one or more proteins that bind to DNA ends.
	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.

Asymmetric Unit
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	Sites
(no "Sites" information available for 2qm4)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2qm4)

Biological Units
	Complete Structure
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Access by PDB/NDB ID
	2qm4
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
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	NHEJ1_HUMAN \| Q9H9Q4
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		Pathway	:	KEGG \| MetaCyc

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	611291
		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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Access by UniProt ID/Accession number
	NHEJ1_HUMAN \| Q9H9Q4
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UniProtKB/Swiss-Prot
	NHEJ1_HUMAN \| Q9H9Q4	:	2r9a 3q4f 3rwr 3sr2 3w03

1fu1	CRYSTAL STRUCTURE OF HUMAN XRCC4
1ik9	CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 36)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 15)

PROSITE Motifs (0, 0)

Exons (5, 20)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (2, 8)

Pfam Domains (1, 4)

Gene Ontology (15, 15)

Visualization

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Still Images

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Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File