3SR2 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN XLF-XRCC4 COMPLEX

Authors :   M. Hammel, S. Classen, J. A. Tainer

Date :   06 Jul 11 (Deposition) - 20 Jul 11 (Release) - 28 Sep 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.97

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H  (1x)
Biol. Unit 2: A,B  (1x)
Biol. Unit 3: C,D  (1x)
Biol. Unit 4: E,F  (1x)
Biol. Unit 5: G,H  (1x)

Keywords :   Xrcc4, Xlf, Nhej, Dna Repair, Dna, Dna Ligases, Dna-Binding Proteins, Dimerization, Humans, Protein Structure, Quaternary, Complex, Non- Homologous End Joining (Nhej), Dna Ligase Iv, Ku, Xlf-Xrcc4, Protein Dna-Interaction, Dna Binding Protein-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Hammel, M. Rey, Y. Yu, R. S. Mani, S. Classen, M. Liu, M. E. Pique, S. Fang, B. L. Mahaney, M. Weinfeld, D. C. Schriemer, S. P. Lees-Miller J. A. Tainer
Xrcc4 Protein Interactions With Xrcc4-Like Factor (Xlf) Create An Extended Grooved Scaffold For Dna Ligation And Double Strand Break Repair.
J. Biol. Chem. V. 286 32638 2011
PubMed-ID: 21775435 | Reference-DOI: 10.1074/JBC.M111.272641

Molecule 1 - DNA REPAIR PROTEIN XRCC4
	Chains	:	A, B, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	ROSETTA2(DE3) PLYSS
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	XRCC4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 4

Molecule 2 - NON-HOMOLOGOUS END-JOINING FACTOR 1
	Chains	:	C, D, G, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	ROSETTA2(DE3) PLYSS
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-224
	Gene	:	NHEJ1, XLF
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN CERNUNNOS, XRCC4-LIKE FACTOR

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B	C	D	E	F	G	H
Biological Unit 2 (1x)	:	A	B
Biological Unit 3 (1x)	:			C	D
Biological Unit 4 (1x)	:					E	F
Biological Unit 5 (1x)	:							G	H

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3SR2)

(no "Site" information available for 3SR2)

(no "SS Bond" information available for 3SR2)

Asymmetric Unit

No.	Residues
1	Asp A:103	-	Val A:104
2	Asp B:103	-	Val B:104
3	Leu D:83	-	Leu D:84

Asymmetric Unit (7, 28)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_022310	S	12	C	XRCC4_HUMAN	Polymorphism	28383138	A/B/E/F	S	12	C
2	UniProt	VAR_038790	A	14	T	NHEJ1_HUMAN	Polymorphism	34689457	C/D/G/H	A	14	T
3	UniProt	VAR_075822	W	43	R	XRCC4_HUMAN	Disease (SSMED)	587779351	A/B/E/F	W	43	R
4	UniProt	VAR_022311	A	56	T	XRCC4_HUMAN	Polymorphism	28383151	A/B/E/F	A	56	T
5	UniProt	VAR_025704	R	57	G	NHEJ1_HUMAN	Disease (NHEJ1-SCID)	118204451	C/D/G/H	R	57	G
6	UniProt	VAR_025705	C	123	R	NHEJ1_HUMAN	Disease (NHEJ1-SCID)	118204452	C/D/G/H	C	123	R
7	UniProt	VAR_022312	I	134	T	XRCC4_HUMAN	Polymorphism	28360135	A/B/E/F	I	134	T

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

Biological Unit 1 (7, 28)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_022310	S	12	C	XRCC4_HUMAN	Polymorphism	28383138	A/B/E/F	S	12	C
2	UniProt	VAR_038790	A	14	T	NHEJ1_HUMAN	Polymorphism	34689457	C/D/G/H	A	14	T
3	UniProt	VAR_075822	W	43	R	XRCC4_HUMAN	Disease (SSMED)	587779351	A/B/E/F	W	43	R
4	UniProt	VAR_022311	A	56	T	XRCC4_HUMAN	Polymorphism	28383151	A/B/E/F	A	56	T
5	UniProt	VAR_025704	R	57	G	NHEJ1_HUMAN	Disease (NHEJ1-SCID)	118204451	C/D/G/H	R	57	G
6	UniProt	VAR_025705	C	123	R	NHEJ1_HUMAN	Disease (NHEJ1-SCID)	118204452	C/D/G/H	C	123	R
7	UniProt	VAR_022312	I	134	T	XRCC4_HUMAN	Polymorphism	28360135	A/B/E/F	I	134	T

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

Biological Unit 2 (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_022310	S	12	C	XRCC4_HUMAN	Polymorphism	28383138	A/B	S	12	C
3	UniProt	VAR_075822	W	43	R	XRCC4_HUMAN	Disease (SSMED)	587779351	A/B	W	43	R
4	UniProt	VAR_022311	A	56	T	XRCC4_HUMAN	Polymorphism	28383151	A/B	A	56	T
7	UniProt	VAR_022312	I	134	T	XRCC4_HUMAN	Polymorphism	28360135	A/B	I	134	T

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

Biological Unit 3 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
2	UniProt	VAR_038790	A	14	T	NHEJ1_HUMAN	Polymorphism	34689457	C/D	A	14	T
5	UniProt	VAR_025704	R	57	G	NHEJ1_HUMAN	Disease (NHEJ1-SCID)	118204451	C/D	R	57	G
6	UniProt	VAR_025705	C	123	R	NHEJ1_HUMAN	Disease (NHEJ1-SCID)	118204452	C/D	C	123	R

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

Biological Unit 4 (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_022310	S	12	C	XRCC4_HUMAN	Polymorphism	28383138	E/F	S	12	C
3	UniProt	VAR_075822	W	43	R	XRCC4_HUMAN	Disease (SSMED)	587779351	E/F	W	43	R
4	UniProt	VAR_022311	A	56	T	XRCC4_HUMAN	Polymorphism	28383151	E/F	A	56	T
7	UniProt	VAR_022312	I	134	T	XRCC4_HUMAN	Polymorphism	28360135	E/F	I	134	T

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

Biological Unit 5 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
2	UniProt	VAR_038790	A	14	T	NHEJ1_HUMAN	Polymorphism	34689457	G/H	A	14	T
5	UniProt	VAR_025704	R	57	G	NHEJ1_HUMAN	Disease (NHEJ1-SCID)	118204451	G/H	R	57	G
6	UniProt	VAR_025705	C	123	R	NHEJ1_HUMAN	Disease (NHEJ1-SCID)	118204452	G/H	C	123	R

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

(no "PROSITE Motif" information available for 3SR2)

Asymmetric Unit (8, 32)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000338635	1b	ENSE00001556292	chr5:82373346-82373434	89	XRCC4_HUMAN	-	0	0	-	-
1.2b	ENST00000338635	2b	ENSE00002174590	chr5:82400729-82400877	149	XRCC4_HUMAN	1-47	47	4	A:1-47 B:1-47 E:1-47 F:1-47	47 47 47 47
1.3a	ENST00000338635	3a	ENSE00000971597	chr5:82406847-82407022	176	XRCC4_HUMAN	47-105	59	4	A:47-105 B:47-105 E:47-105 F:47-105	59 59 59 59
1.4	ENST00000338635	4	ENSE00001005114	chr5:82491589-82491755	167	XRCC4_HUMAN	106-161	56	4	A:106-139 B:106-140 E:106-140 F:106-140	34 35 35 35
1.5	ENST00000338635	5	ENSE00001005109	chr5:82499371-82499526	156	XRCC4_HUMAN	161-213	53	0	-	-
1.6	ENST00000338635	6	ENSE00001005110	chr5:82500634-82500740	107	XRCC4_HUMAN	213-249	37	0	-	-
1.7a	ENST00000338635	7a	ENSE00001005113	chr5:82554349-82554496	148	XRCC4_HUMAN	249-298	50	0	-	-
1.8a	ENST00000338635	8a	ENSE00001932573	chr5:82648944-82649530	587	XRCC4_HUMAN	298-336	39	0	-	-

2.1b	ENST00000356853	1b	ENSE00001869065	chr2:220025575-220025442	134	NHEJ1_HUMAN	-	0	0	-	-
2.4b	ENST00000356853	4b	ENSE00002167216	chr2:220023084-220022908	177	NHEJ1_HUMAN	1-59	59	4	C:1-59 D:1-59 G:1-59 H:1-59	59 59 59 59
2.5a	ENST00000356853	5a	ENSE00001708572	chr2:220022406-220022194	213	NHEJ1_HUMAN	60-130	71	4	C:60-130 (gaps) D:60-130 (gaps) G:60-130 (gaps) H:60-130 (gaps)	71 71 71 71
2.6	ENST00000356853	6	ENSE00001664826	chr2:220012517-220012379	139	NHEJ1_HUMAN	131-177	47	4	C:131-177 D:131-177 G:131-177 H:131-177	47 47 47 47
2.7b	ENST00000356853	7b	ENSE00001631569	chr2:220011460-220011402	59	NHEJ1_HUMAN	177-196	20	4	C:177-196 D:177-196 G:177-196 H:177-196	20 20 20 20
2.11b	ENST00000356853	11b	ENSE00001776599	chr2:219942928-219942811	118	NHEJ1_HUMAN	197-236	40	4	C:197-224 D:197-224 G:197-224 H:197-224	28 28 28 28
2.12	ENST00000356853	12	ENSE00001706214	chr2:219942086-219941968	119	NHEJ1_HUMAN	236-275	40	0	-	-
2.13f	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:139
 aligned with XRCC4_HUMAN | Q13426 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         
          XRCC4_HUMAN     1 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQA 139
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...........eeeeee..hhhhheeeeee....eeeeee.hhhhhhhhhhhh.hhhhhhhhhhhhh........eeeeee.....eeeeeee......eeeeee.ee..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------C------------------------------R------------T-----------------------------------------------------------------------------T----- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:1-47 UniProt: 1-47           ----------------------------------------------------------Exon 1.4  PDB: A:106-139           Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.3a  PDB: A:47-105 UniProt: 47-105                   ---------------------------------- Transcript 1 (2)
                 3sr2 A   1 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQA 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:140
 aligned with XRCC4_HUMAN | Q13426 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
          XRCC4_HUMAN     1 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQAK 140
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...........eeeeee..hhh.eeeeeee....eeeeeeehhhhhhhhhhh..hhhhhhhhhhhh.........eeeeeee....eeeeeee......eeeeee.....hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -----------C------------------------------R------------T-----------------------------------------------------------------------------T------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: B:1-47 UniProt: 1-47           ----------------------------------------------------------Exon 1.4  PDB: B:106-140            Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.3a  PDB: B:47-105 UniProt: 47-105                   ----------------------------------- Transcript 1 (2)
                 3sr2 B   1 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQAK 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain C from PDB  Type:PROTEIN  Length:218
 aligned with NHEJ1_HUMAN | Q9H9Q4 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
          NHEJ1_HUMAN     1 MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQ 224
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..ee........eeeeeee..eeeeeee....eeeeeeehhhhhhhhh........hhhhhhhhhhhhhhhhhh------...eeeeee..eeeeeeeee....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------T------------------------------------------G-----------------------------------------------------------------R----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.4b  PDB: C:1-59 UniProt: 1-59                       Exon 2.5a  PDB: C:60-130 (gaps) UniProt: 60-130                        Exon 2.6  PDB: C:131-177 UniProt: 131-177      -------------------Exon 2.11b  PDB: C:197-224   Transcript 2 (1)
           Transcript 2 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 2.7b           ---------------------------- Transcript 2 (2)
                 3sr2 C   1 MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLK------EATFSCDCVADALILRVRSELSGLPFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQ 224
                                    10        20        30        40        50        60        70        80    |    - |     100       110       120       130       140       150       160       170       180       190       200       210       220    
                                                                                                               85     92

Chain D from PDB  Type:PROTEIN  Length:218
 aligned with NHEJ1_HUMAN | Q9H9Q4 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
          NHEJ1_HUMAN     1 MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQ 224
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..ee........eeeeee...eeeeeee....eeeeeeehhhhhhhhhhhh.....hhhhhhhhhhh........------.eeeeeee..eeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------T------------------------------------------G-----------------------------------------------------------------R----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.4b  PDB: D:1-59 UniProt: 1-59                       Exon 2.5a  PDB: D:60-130 (gaps) UniProt: 60-130                        Exon 2.6  PDB: D:131-177 UniProt: 131-177      -------------------Exon 2.11b  PDB: D:197-224   Transcript 2 (1)
           Transcript 2 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 2.7b           ---------------------------- Transcript 2 (2)
                 3sr2 D   1 MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKD------ATFSCDCVADALILRVRSELSGLPFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQ 224
                                    10        20        30        40        50        60        70        80     |   -  |    100       110       120       130       140       150       160       170       180       190       200       210       220    
                                                                                                                86     93

Chain E from PDB  Type:PROTEIN  Length:140
 aligned with XRCC4_HUMAN | Q13426 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
          XRCC4_HUMAN     1 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQAK 140
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeeeee..hhhh.eeeeee....eeeeeehhhhhhhhhhhhh.hhhhhhhhhhh..........eeeee......eeeeeee........eeee.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------C------------------------------R------------T-----------------------------------------------------------------------------T------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: E:1-47 UniProt: 1-47           ----------------------------------------------------------Exon 1.4  PDB: E:106-140            Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.3a  PDB: E:47-105 UniProt: 47-105                   ----------------------------------- Transcript 1 (2)
                 3sr2 E   1 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQAK 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain F from PDB  Type:PROTEIN  Length:140
 aligned with XRCC4_HUMAN | Q13426 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
          XRCC4_HUMAN     1 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQAK 140
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...........eeeeee.......eeeeee....eeeeeehhhhhhhhhhhhh.hhhhhhhhh............eeeee.......eeeeeee..ee...eee..ee..hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------C------------------------------R------------T-----------------------------------------------------------------------------T------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: F:1-47 UniProt: 1-47           ----------------------------------------------------------Exon 1.4  PDB: F:106-140            Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.3a  PDB: F:47-105 UniProt: 47-105                   ----------------------------------- Transcript 1 (2)
                 3sr2 F   1 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQAK 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain G from PDB  Type:PROTEIN  Length:217
 aligned with NHEJ1_HUMAN | Q9H9Q4 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
          NHEJ1_HUMAN     1 MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQ 224
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh...ee........eeeeee....eeeeee....eeeeee.hhhhhhh..........hhhhhhhhhhhhhh...-------..eeeeeee..eeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------T------------------------------------------G-----------------------------------------------------------------R----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.4b  PDB: G:1-59 UniProt: 1-59                       Exon 2.5a  PDB: G:60-130 (gaps) UniProt: 60-130                        Exon 2.6  PDB: G:131-177 UniProt: 131-177      -------------------Exon 2.11b  PDB: G:197-224   Transcript 2 (1)
           Transcript 2 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 2.7b           ---------------------------- Transcript 2 (2)
                 3sr2 G   1 MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLL-------EATFSCDCVADALILRVRSELSGLPFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQ 224
                                    10        20        30        40        50        60        70        80   |     - |     100       110       120       130       140       150       160       170       180       190       200       210       220    
                                                                                                              84      92

Chain H from PDB  Type:PROTEIN  Length:220
 aligned with NHEJ1_HUMAN | Q9H9Q4 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:226
                              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     - --MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQ 224
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..............eeeeee...eeeeeee....eeeeeeehhhhhhhhhhhh.....hhhhhhhhhhh.....------....eeeee......eeeeee......eeeeee.ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhh.........hhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------T------------------------------------------G-----------------------------------------------------------------R----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) --Exon 2.4b  PDB: H:1-59 UniProt: 1-59                       Exon 2.5a  PDB: H:60-130 (gaps) UniProt: 60-130                        Exon 2.6  PDB: H:131-177 UniProt: 131-177      -------------------Exon 2.11b  PDB: H:197-224   Transcript 2 (1)
           Transcript 2 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 2.7b           ---------------------------- Transcript 2 (2)
                 3sr2 H  -1 GSMEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPL------PSEATFSCDCVADALILRVRSELSGLPFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQ 224
                                     8        18        28        38        48        58        68        78    |    - |      98       108       118       128       138       148       158       168       178       188       198       208       218      
                                                                                                               83     90

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 3SR2)

(no "CATH Domain" information available for 3SR2)

(no "Pfam Domain" information available for 3SR2)

Asymmetric Unit(hide GO term definitions)

Chain A,B,E,F (XRCC4_HUMAN | Q13426)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	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: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:0051103	DNA ligation involved in DNA repair	The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA repair.
	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: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:0071285	cellular response to lithium ion	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 lithium (Li+) ion stimulus.
	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:0075713	establishment of integrated proviral latency	A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
	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: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:0010165	response to X-ray	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 X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz).
cellular component
	GO:0032807	DNA ligase IV complex	A eukaryotically conserved protein complex that contains DNA ligase IV and is involved in DNA repair by non-homologous end joining; in addition to the ligase, the complex also contains XRCC4 or a homolog, e.g. Saccharomyces Lif1p.
	GO:0005958	DNA-dependent protein kinase-DNA ligase 4 complex	A large protein complex which is involved in the repair of DNA double-strand breaks and, in mammals, V(D)J recombination events. It consists of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), the DNA end-binding heterodimer Ku, the nuclear phosphoprotein XRCC4 or a homolog thereof, and DNA ligase IV.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0000793	condensed chromosome	A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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.

Chain C,D,G,H (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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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3sr2)

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(no "Sites" information available for 3sr2)

	Cis Peptide Bonds
		Asp A:103 - Val A:104	[ RasMol ]
		Asp B:103 - Val B:104	[ RasMol ]
		Leu D:83 - Leu D:84	[ RasMol ]

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	3sr2
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	XRCC4_HUMAN \| Q13426
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(no "Related Entries Specified in the PDB File" available for 3SR2)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 28)

PROSITE Motifs (0, 0)

Exons (8, 32)

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