4A09 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF HSDDB1-DRDDB2 BOUND TO A 15 BP CPD-DUPLEX (PURINE AT D-1 POSITION) AT 3.1 A RESOLUTION (CPD 2)

Authors :   A. Scrima, E. S. Fischer, S. Iwai, H. Gut, N. H. Thoma

Date :   08 Sep 11 (Deposition) - 30 Nov 11 (Release) - 07 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym./Biol. Unit : A,B,G,H

Keywords :   Dna-Binding Protein-Dna Complex, Dna Damage Repair, Ddb (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Scrima, E. S. Fischer, S. Iwai, H. Gut, N. H. Thoma
The Molecular Basis Of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, And Activation
Cell(Cambridge, Mass. ) V. 147 1024 2011
PubMed-ID: 22118460 | Reference-DOI: 10.1016/J.CELL.2011.10.035

Molecule 1 - DNA DAMAGE-BINDING PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	BTI TN 5B1 4
	Expression System Common	:	CABBAGE LOOPER
	Expression System Plasmid	:	PFASTBAC DERIVED
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DDB P127 SUBUNIT, DNA DAMAGE-BINDING PROTEIN A, DDBA, DAMAGE-SPECIFIC DNA-BINDING PROTEIN 1, HBV X-ASSOCIATED PROTEIN 1, XAP-1, UV-DAMAGED DNA-BINDING FACTOR, UV-DAMAGED DNA-BINDING PROTEIN 1, UV-DDB 1, XPE-BINDING FACTOR, XPE-BF, XERODERMA PIGMENTOSUM GROUP E-COMPLEMENTING PROTEIN, XPCE

Molecule 2 - DNA DAMAGE-BINDING PROTEIN 2
	Chains	:	B
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	BTI TN 5B1 4
	Expression System Common	:	CABBAGE LOOPER
	Expression System Plasmid	:	PFASTBAC DERIVED
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	RESIDUES 60-423
	Organism Common	:	ZEBRAFISH
	Organism Scientific	:	DANIO RERIO
	Organism Taxid	:	7955
	Synonym	:	DAMAGE-SPECIFIC DNA-BINDING PROTEIN 2

*Molecule 3 - 5'-D(GPGPTPGPAPAPAP(TTD)PAPGPCPAPGPGP)-3'*
	Chains	:	G
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Other Details	:	DAMAGED STRAND. CONTAINS CYCLOBUTANE PYRIMIDINE DIMER (CPD)
	Synthetic	:	YES

*Molecule 4 - 5'-D(CPCPTPGPCPTPCPCPTPTPTPCPAPCPCPC)-3'*
	Chains	:	H
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Other Details	:	UNDAMAGED STRAND
	Synthetic	:	YES

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	TTD	1	Mod. Nucleotide	CIS-SYN CYCLOBUTANE THYMINE DIMER

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR B:331	BINDING SITE FOR RESIDUE CA B1456

(no "SS Bond" information available for 4A09)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:224	-	Pro A:225
2	Gly A:357	-	Pro A:358

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_023074	L	427	F	DDB1_HUMAN	Polymorphism	28720299	A	L	427	F

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	WD_REPEATS_1	PS00678	Trp-Asp (WD) repeats signature.	DDB2_DANRE	260-274	1	B:294-308

Asymmetric/Biological Unit (27, 27)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000301764	1a	ENSE00001766096	chr11:61100666-61100380	287	DDB1_HUMAN	1-21	21	1	A:1-21	21
1.2	ENST00000301764	2	ENSE00001244589	chr11:61099163-61099015	149	DDB1_HUMAN	21-70	50	1	A:21-70	50
1.3c	ENST00000301764	3c	ENSE00001244580	chr11:61097546-61097430	117	DDB1_HUMAN	71-109	39	1	A:71-109	39
1.4	ENST00000301764	4	ENSE00001244572	chr11:61097056-61096835	222	DDB1_HUMAN	110-183	74	1	A:110-183	74
1.5	ENST00000301764	5	ENSE00001119057	chr11:61094365-61094251	115	DDB1_HUMAN	184-222	39	1	A:184-222	39
1.6a	ENST00000301764	6a	ENSE00001119056	chr11:61093180-61093083	98	DDB1_HUMAN	222-254	33	1	A:222-254	33
1.7	ENST00000301764	7	ENSE00001119058	chr11:61091609-61091451	159	DDB1_HUMAN	255-307	53	1	A:255-307 (gaps)	53
1.8	ENST00000301764	8	ENSE00001119055	chr11:61090566-61090483	84	DDB1_HUMAN	308-335	28	1	A:308-335	28
1.9	ENST00000301764	9	ENSE00001119053	chr11:61089884-61089768	117	DDB1_HUMAN	336-374	39	1	A:336-374	39
1.10a	ENST00000301764	10a	ENSE00001119059	chr11:61089169-61089067	103	DDB1_HUMAN	375-409	35	1	A:375-409	35
1.11	ENST00000301764	11	ENSE00001145160	chr11:61084039-61083964	76	DDB1_HUMAN	409-434	26	1	A:409-434	26
1.12	ENST00000301764	12	ENSE00001145157	chr11:61083865-61083757	109	DDB1_HUMAN	434-470	37	1	A:434-470	37
1.13	ENST00000301764	13	ENSE00001198138	chr11:61081958-61081780	179	DDB1_HUMAN	471-530	60	1	A:471-530	60
1.14	ENST00000301764	14	ENSE00001063042	chr11:61081682-61081519	164	DDB1_HUMAN	530-585	56	1	A:530-585	56
1.15	ENST00000301764	15	ENSE00001063027	chr11:61081441-61081334	108	DDB1_HUMAN	585-621	37	1	A:585-621	37
1.16	ENST00000301764	16	ENSE00001063028	chr11:61081178-61080971	208	DDB1_HUMAN	621-690	70	1	A:621-690	70
1.17	ENST00000301764	17	ENSE00001145124	chr11:61079556-61079461	96	DDB1_HUMAN	690-722	33	1	A:690-722	33
1.18	ENST00000301764	18	ENSE00001198106	chr11:61079367-61079256	112	DDB1_HUMAN	722-759	38	1	A:722-759	38
1.19	ENST00000301764	19	ENSE00001063044	chr11:61077890-61077767	124	DDB1_HUMAN	760-801	42	1	A:760-801 (gaps)	42
1.20	ENST00000301764	20	ENSE00001063040	chr11:61077432-61077268	165	DDB1_HUMAN	801-856	56	1	A:801-856	56
1.21	ENST00000301764	21	ENSE00001063041	chr11:61076549-61076455	95	DDB1_HUMAN	856-887	32	1	A:856-887	32
1.22	ENST00000301764	22	ENSE00001145096	chr11:61071507-61071337	171	DDB1_HUMAN	888-944	57	1	A:888-944	57
1.23	ENST00000301764	23	ENSE00001145090	chr11:61070627-61070518	110	DDB1_HUMAN	945-981	37	1	A:945-981	37
1.24	ENST00000301764	24	ENSE00001198074	chr11:61070223-61070054	170	DDB1_HUMAN	981-1038	58	1	A:981-1038 (gaps)	58
1.25	ENST00000301764	25	ENSE00001506453	chr11:61069831-61069729	103	DDB1_HUMAN	1038-1072	35	1	A:1038-1072	35
1.26	ENST00000301764	26	ENSE00001506452	chr11:61068404-61068281	124	DDB1_HUMAN	1072-1113	42	1	A:1072-1111	40
1.27b	ENST00000301764	27b	ENSE00001798842	chr11:61067691-61066920	772	DDB1_HUMAN	1114-1140	27	1	A:1123-1140	18

Asymmetric/Biological 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:1105
 aligned with DDB1_HUMAN | Q16531 from UniProtKB/Swiss-Prot  Length:1140

    Alignment length:1140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140
          DDB1_HUMAN      1 MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVACLDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSHYLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH 1140
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee......eeeee........eeeeee..eeeeeeee..eeeeeeeee....eeeeeee........eeeeee...eeeeeeeeee..eeeeeeeeeee.............eeee.....eeeee....eeeeee..........eeee....eeeeeee.......eeeeeeee..eeeeeeeeee....eeee.....ee......eeee.......eeee....eeeee..eeeee...hhhhh.eeeeee......eeeeee...eeeeeeeeee.-----.eeeeeeeeeeee...eeeeeeee..eeeeee....eeeeee..........eeeeeee.....eeeeeee........eeeeee.hhhh.eeeeeee...eeeeeee.......eeee..........eeeee....eeeeeee..eeee...........eeeeeee...eeeeee..eeeee......eeeeee........eeee...eeeeee..eeeeeeee..eeeeeeeee....eeeee............eeeeee.....eeeee.....eee.........eeeeeeeee..eeeeeeee...eeeeeee......eeeeeeee......eeeeee....eeeeee....eeeeee..eeeeee.......eeeee.......eeeee....eeeeee.....eeeeeee...eeeeeeee....eeeeeeeeeeee.....eee..........eeee......------------..eeeeeeeeee.....eeeeee....eeeeeeeee........eeeeeeee..........eeeeeeeee..eeeeeeeeee...eeeeeee..eeeeee..eeeeeee.....eeeeeee.....eeeeeee..eeeeee....eeeeeee....eeeeeee......eeeeeeee..eeeeee...eeeeeee.....hhhhhh.eeeeeeee....eeeeee......-------.....eeeee....eeeeee.hhhhhhhhhhhhhhhhhhh......hhhhhh.ee....ee....eeehhhhhhhhhhhhhhhhhhh..-----------..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:1-2-------------------------------------------------Exon 1.3c  PDB: A:71-109               Exon 1.4  PDB: A:110-183 UniProt: 110-183                                 Exon 1.5  PDB: A:184-222               --------------------------------Exon 1.7  PDB: A:255-307 (gaps) UniProt: 255-307     Exon 1.8  PDB: A:308-335    Exon 1.9  PDB: A:336-374               Exon 1.10a  PDB: A:375-409         ------------------------Exon 1.12  PDB: A:434-470            Exon 1.13  PDB: A:471-530 UniProt: 471-530                  ------------------------------------------------------Exon 1.15  PDB: A:585-621            --------------------------------------------------------------------Exon 1.17  PDB: A:690-722        -------------------------------------Exon 1.19  PDB: A:760-801 (gaps)          ------------------------------------------------------Exon 1.21  PDB: A:856-887       Exon 1.22  PDB: A:888-944 UniProt: 888-944               Exon 1.23  PDB: A:945-981            --------------------------------------------------------Exon 1.25  PDB: A:1038-1072        -----------------------------------------Exon 1.27b  PDB: A:1123-114 Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.2  PDB: A:21-70 UniProt: 21-70             -------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6a  PDB: A:222-254        ----------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.11  PDB: A:409-434 -----------------------------------------------------------------------------------------------Exon 1.14  PDB: A:530-585 UniProt: 530-585              -----------------------------------Exon 1.16  PDB: A:621-690 UniProt: 621-690                            -------------------------------Exon 1.18  PDB: A:722-759             -----------------------------------------Exon 1.20  PDB: A:801-856 UniProt: 801-856              ----------------------------------------------------------------------------------------------------------------------------Exon 1.24  PDB: A:981-1038 (gaps) UniProt: 981-1038       ---------------------------------Exon 1.26  PDB: A:1072-1111 [INCOMPLETE]  --------------------------- Transcript 1 (2)
                4a09 A    1 MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYAVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEE-----VTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVACLDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSHYLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLF------------EEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQ-------PTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVAN-----------EATADDLIKVVEELTRIH 1140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        |-    |  300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770|        -   |   790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010    |    -  |   1030      1040      1050      1060      1070      1080      1090      1100      1110|        -  |   1130      1140
                                                                                                                                                                                                                                                                                                                          289   295                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         771          784                                                                                                                                                                                                                                   1015    1023                                                                                    1111        1123

Chain B from PDB  Type:PROTEIN  Length:354
 aligned with DDB2_DANRE | Q2YDS1 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:354
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417    
          DDB2_DANRE     68 QTSILHYIYKSSLGQSIHAQLRQCLQEPFIRSLKSYKLHRTASPFDRRVTSLEWHPTHPTTVAVGSKGGDIILWDYDVLNKTSFIQGMGPGDAITGMKFNQFNTNQLFVSSIWGATTLRDFSGSVIQVFAKTDSWDYWYCCVDVSVSRQMLATGDSTGRLLLLGLDGHEIFKEKLHKAKVTHAEFNPRCDWLMATSSVDATVKLWDLRNIKDKNSYIAEMPHEKPVNAAYFNPTDSTKLLTTDQRNEIRVYSSYDWSKPDQIIIHPHRQFQHLTPIKATWHPMYDLIVAGRYPDDQLLLNDKRTIDIYDANSGGLVHQLRDPNAAGIISLNKFSPTGDVLASGMGFNILIWNRE  421
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhheeeeee......eeeeee......eeeeee....eeeee.......eee........eeeeee......eeeeee...eeeeee....eeeeee........eeeeeee....eeeeee...eeeeee....eeeeee.....eeeeeee..eeeeeeeee...eeeeee.........eeeeee....eeeeee......eeeeee...eeeeee........eeee..............ee.....eeeee..............eeeee.....eeeee..........eeee......eeeee..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD_REPEATS_1   --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4a09 B  102 QTSILHYIYKSSLGQSIHAQLRQCLQEPFIRSLKSYKLHRTASPFDRRVTSLEWHPTHPTTVAVGSKGGDIILWDYDVQNKTSFIQGMGPGDAITGMKFNQFNTNQLFVSSIRGATTLRDFSGSVIQVFAKTDSWDYWYCCVDVSVSRQMLATGDSTGRLLLLGLDGHEIFKEKLHKAKVTHAEFNPRCDWLMATSSVDATVKLWDLRNIKDKNSYIAEMPHEKPVNAAYFNPTDSTKLLTTDQRNEIRVYSSYDWSKPDQIIIHPHRQFQHLTPIKATWHPMYDLIVAGRYPDDQLLLNDKRTIDIYDANSGGLVHQLRDPNAAGIISLNKFSPTGDVLASGMGFNILIWNRE  455
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451

Chain G from PDB  Type:DNA  Length:14
                                               
                4a09 G    1 GGTGAAAtAGCAGG   15
                                   |11    
                                   8-TTD  
                                   10

Chain H from PDB  Type:DNA  Length:15
                                                
                4a09 H    1 CCTGCTCCTTTCACC   15
                                    10

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 4A09)

(no "CATH Domain" information available for 4A09)

(no "Pfam Domain" information available for 4A09)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DDB1_HUMAN | Q16531)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0042769	DNA damage response, detection of DNA damage	The series of events required to receive a stimulus indicating DNA damage has occurred and convert it to a molecular signal.
	GO: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:0070914	UV-damage excision repair	A DNA repair process that is initiated by an endonuclease that introduces a single-strand incision immediately 5' of a UV-induced damage site. UV-damage excision repair acts on both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone 6-4 photoproducts (6-4PPs).
	GO:0016055	Wnt signaling pathway	The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
	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:0070911	global genome nucleotide-excision repair	The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
	GO:0035518	histone H2A monoubiquitination	The modification of histone H2A by addition of a single ubiquitin group.
	GO:0051702	interaction with symbiont	An interaction between two organisms living together in more or less intimate association. The term symbiont is used for the smaller (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0006289	nucleotide-excision repair	A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
	GO:0000715	nucleotide-excision repair, DNA damage recognition	The identification of lesions in DNA, such as pyrimidine-dimers, intrastrand cross-links, and bulky adducts. The wide range of substrate specificity suggests the repair complex recognizes distortions in the DNA helix.
	GO:0000717	nucleotide-excision repair, DNA duplex unwinding	The unwinding, or local denaturation, of the DNA duplex to create a bubble around the site of the DNA damage.
	GO:0033683	nucleotide-excision repair, DNA incision	A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.
	GO:0006295	nucleotide-excision repair, DNA incision, 3'-to lesion	The endonucleolytic cleavage of the damaged strand of DNA 3' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision precedes the incision formed 5' to the site of damage.
	GO:0006296	nucleotide-excision repair, DNA incision, 5'-to lesion	The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage.
	GO:0006294	nucleotide-excision repair, preincision complex assembly	The aggregation, arrangement and bonding together of proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
	GO:0006293	nucleotide-excision repair, preincision complex stabilization	The stabilization of the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage as well as the unwound DNA. The stabilization of the protein-DNA complex ensures proper positioning of the preincision complex before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
	GO:0046726	positive regulation by virus of viral protein levels in host cell	Any process where the infecting virus increases the levels of viral proteins in a cell.
	GO:0045070	positive regulation of viral genome replication	Any process that activates or increases the frequency, rate or extent of viral genome replication.
	GO:1902188	positive regulation of viral release from host cell	Any process that activates or increases the frequency, rate or extent of viral release from host cell.
	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0042787	protein ubiquitination involved in ubiquitin-dependent protein catabolic process	The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
	GO:1901990	regulation of mitotic cell cycle phase transition	Any process that modulates the frequency, rate or extent of mitotic cell cycle phase transition.
	GO:0006283	transcription-coupled nucleotide-excision repair	The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0080008	Cul4-RING E3 ubiquitin ligase complex	A ubiquitin ligase complex in which a cullin from the Cul4 family and a RING domain protein form the catalytic core; substrate specificity is conferred by an adaptor protein.
	GO:0031464	Cul4A-RING E3 ubiquitin ligase complex	A ubiquitin ligase complex in which a cullin from the Cul4A subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by an adaptor protein.
	GO:0031465	Cul4B-RING E3 ubiquitin ligase complex	A ubiquitin ligase complex in which a cullin from the Cul4B subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by unknown subunits.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain B (DDB2_DANRE | Q2YDS1)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
biological process
	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:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
cellular component
	GO:0080008	Cul4-RING E3 ubiquitin ligase complex	A ubiquitin ligase complex in which a cullin from the Cul4 family and a RING domain protein form the catalytic core; substrate specificity is conferred by an adaptor protein.
	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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	4a09
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2b5l	CRYSTAL STRUCTURE OF DDB1 IN COMPLEX WITH SIMIAN VIRUS 5 VPROTEIN
2b5m	CRYSTAL STRUCTURE OF DDB1
2b5n	CRYSTAL STRUCTURE OF THE DDB1 BPB DOMAIN
2hye	CRYSTAL STRUCTURE OF THE DDB1-CUL4A-RBX1-SV5V COMPLEX
3ei1
3ei2
3ei3
3ei4
4a08	STRUCTURE OF HSDDB1-DRDDB2 BOUND TO A 13 BP CPD- DUPLEX (PURINE AT D-1 POSITION) AT 3.0 A RESOLUTION (CPD 1)
4a0a	STRUCTURE OF HSDDB1-DRDDB2 BOUND TO A 16 BP CPD- DUPLEX (PYRIMIDINE AT D-1 POSITION) AT 3.6 A RESOLUTION (CPD 3)
4a0b	STRUCTURE OF HSDDB1-DRDDB2 BOUND TO A 16 BP CPD- DUPLEX (PYRIMIDINE AT D-1 POSITION) AT 3.8 A RESOLUTION (CPD 4)
4a0c	STRUCTURE OF THE CAND1-CUL4B-RBX1 COMPLEX
4a0k	STRUCTURE OF DDB1-DDB2-CUL4A-RBX1 BOUND TO A 12 BP ABASIC SITE CONTAINING DNA-DUPLEX
4a0l
4a11

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (27, 27)

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SCOP Domains (0, 0)

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Gene Ontology (39, 46)

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