2J4D - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYPTOCHROME 3 FROM ARABIDOPSIS THALIANA

Authors :   T. Klar, R. Pokorny, A. Batschauer, L. -O. Essen

Date :   28 Aug 06 (Deposition) - 19 Jun 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Dna-Binding Protein, Cryptochrome, Flavoprotein, Fad, Mitochondrion, Plastid, Chromophore, Chloroplast, Transit Peptide, Blue-Light Response (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Klar, R. Pokorny, J. Moldt, A. Batschauer, L. -O. Essen
Cryptochrome 3 From Arabidopsis Thaliana: Structural And Functional Analysis Of Its Complex With A Folate Light Antenna
J. Mol. Biol. V. 366 954 2007
PubMed-ID: 17188299 | Reference-DOI: 10.1016/J.JMB.2006.11.066
(for further references see the PDB file header)

Molecule 1 - CRYPTOCHROME DASH
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE-60
	Expression System Strain	:	M15-PREP4
	Expression System Taxid	:	562
	Fragment	:	MATURE PROTEIN WITHOUT PLASTID IMPORT SEQUENCE, RESIDUES 45-569
	Organism Common	:	MOUSE-EAR CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	CRYPTOCHROME 3

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	MHF	2	Ligand/Ion	5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	MHF	1	Ligand/Ion	5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	MHF	1	Ligand/Ion	5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:272 , SER A:285 , THR A:286 , LYS A:287 , PHE A:288 , SER A:289 , LEU A:292 , GLU A:325 , ARG A:329 , PHE A:388 , ASN A:391 , ARG A:394 , GLN A:395 , LEU A:420 , ASP A:422 , TYR A:423 , ASP A:424 , SER A:427 , ASN A:428 , ASN A:431 , TRP A:432 , HOH A:2302 , HOH A:2346 , HOH A:2380 , HOH A:2394 , HOH A:2429 , HOH A:2430	BINDING SITE FOR RESIDUE FAD A1498
2	AC2	SOFTWARE	HIS A:83 , LYS A:89 , CYS A:146 , SER A:147 , GLU A:148 , GLU A:149 , ASN A:341 , PHE A:344 , HIS A:345 , GLU A:417 , TYR A:423 , PRO A:425 , TYR A:429 , HOH A:2431 , HOH A:2433 , HOH A:2434 , HOH A:2436 , PHE B:188 , ASP B:189 , LYS B:338 , HOH B:2147	BINDING SITE FOR RESIDUE MHF A1499
3	AC3	SOFTWARE	TYR B:272 , SER B:285 , THR B:286 , LYS B:287 , PHE B:288 , SER B:289 , LEU B:292 , GLU B:325 , ARG B:329 , PHE B:332 , PHE B:388 , ASN B:391 , ARG B:394 , LEU B:420 , ASP B:422 , TYR B:423 , ASP B:424 , SER B:427 , ASN B:428 , ASN B:431 , TRP B:432 , HOH B:2197 , HOH B:2278 , HOH B:2303 , HOH B:2304 , HOH B:2305	BINDING SITE FOR RESIDUE FAD B1501
4	AC4	SOFTWARE	PHE A:188 , ASP A:189 , LYS A:338 , HIS B:83 , LYS B:89 , CYS B:146 , SER B:147 , GLU B:148 , GLU B:149 , ASN B:341 , PHE B:344 , HIS B:345 , GLU B:417 , TYR B:423 , PRO B:425 , TYR B:429 , HOH B:2306 , HOH B:2307 , HOH B:2309	BINDING SITE FOR RESIDUE MHF B1502

(no "SS Bond" information available for 2J4D)

Asymmetric Unit

No.	Residues
1	Val A:7	-	Pro A:8
2	Gly A:218	-	Pro A:219
3	Val B:7	-	Pro B:8
4	Gly B:218	-	Pro B:219

(no "SAP(SNP)/Variant" information available for 2J4D)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHR_CRY_ALPHA_BETA	PS51645	Photolyase/cryptochrome alpha/beta domain profile.	CRYD_ARATH	84-221	2	A:40-177 B:40-177

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHR_CRY_ALPHA_BETA	PS51645	Photolyase/cryptochrome alpha/beta domain profile.	CRYD_ARATH	84-221	1	A:40-177 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHR_CRY_ALPHA_BETA	PS51645	Photolyase/cryptochrome alpha/beta domain profile.	CRYD_ARATH	84-221	1	- B:40-177

(no "Exon" information available for 2J4D)

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:496
 aligned with CRYD_ARATH | Q84KJ5 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:496
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535      
           CRYD_ARATH    46 DHIHRVPALTEEEIDSVAIKTFERYALPSSSSVKRKGKGVTILWFRNDLRVLDNDALYKAWSSSDTILPVYCLDPRLFHTTHFFNFPKTGALRGGFLMECLVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGARTVFAHKETCSEEVDVERLVNQGLKRVGNSTKLELIWGSTMYHKDDLPFDVFDLPDVYTQFRKSVEAKCSIRSSTRIPLSLGPTPSVDDWGDVPTLEKLGVEPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKETRNGMLGPDYSTKFSPWLAFGCISPRFIYEEVQRYEKERVANNSTYWVLFELIWRDYFRFLSIKCGNSLFHLGGPRNVQGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYGAGVGNDPREDRYFSIPKQAQNYDPEGEYVAFWLQQLRRLPKEKRHWPGRLMYMDTVVPLKHG 541
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhhhhh.............eeeeee........hhhhhhhhhh..eeeeeeeehhhhhh..........hhhhhhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh.....eeeee......hhhhh..hhhhh..hhhhhhhhhhhhh.......................................eeee..hhhhhhhhhhhhhh...hhhhhhhhh...........hhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhh...hhhhhhhhhh..hhhhhhhhhhhh.........hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------PHR_CRY_ALPHA_BETA  PDB: A:40-177 UniProt: 84-221                                                                                         -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j4d A   2 DHIHRVPALTEEEIDSVAIKTFERYALPSSSSVKRKGKGVTILWFRNDLRVLDNDALYKAWSSSDTILPVYCLDPRLFHTTHFFNFPKTGALRGGFLMECLVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGARTVFAHKETCSEEVDVERLVNQGLKRVGNSTKLELIWGSTMYHKDDLPFDVFDLPDVYTQFRKSVEAKCSIRSSTRIPLSLGPTPSVDDWGDVPTLEKLGVEPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKETRNGMLGPDYSTKFSPWLAFGCISPRFIYEEVQRYEKERVANNSTYWVLFELIWRDYFRFLSIKCGNSLFHLGGPRNVQGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYGAGVGNDPREDRYFSIPKQAQNYDPEGEYVAFWLQQLRRLPKEKRHWPGRLMYMDTVVPLKHG 497
                                    11        21        31        41        51        61        71        81        91       101       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       461       471       481       491

Chain B from PDB  Type:PROTEIN  Length:499
 aligned with CRYD_ARATH | Q84KJ5 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:499
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535         
           CRYD_ARATH    46 DHIHRVPALTEEEIDSVAIKTFERYALPSSSSVKRKGKGVTILWFRNDLRVLDNDALYKAWSSSDTILPVYCLDPRLFHTTHFFNFPKTGALRGGFLMECLVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGARTVFAHKETCSEEVDVERLVNQGLKRVGNSTKLELIWGSTMYHKDDLPFDVFDLPDVYTQFRKSVEAKCSIRSSTRIPLSLGPTPSVDDWGDVPTLEKLGVEPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKETRNGMLGPDYSTKFSPWLAFGCISPRFIYEEVQRYEKERVANNSTYWVLFELIWRDYFRFLSIKCGNSLFHLGGPRNVQGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYGAGVGNDPREDRYFSIPKQAQNYDPEGEYVAFWLQQLRRLPKEKRHWPGRLMYMDTVVPLKHGNGP 544
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhhhhh.............eeeeee........hhhhhhhhhh..eeeeeeeehhhhhh..........hhhhhhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh.....eeeee......hhhhh..hhhhh..hhhhhhhhhhhhh.......................................eeee..hhhhhhhhhhhhhh...hhhhhhhhh...........hhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhh............hhhhhhhhhh..hhhhhhhhhhhh..hhhhhh.hhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------PHR_CRY_ALPHA_BETA  PDB: B:40-177 UniProt: 84-221                                                                                         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j4d B   2 DHIHRVPALTEEEIDSVAIKTFERYALPSSSSVKRKGKGVTILWFRNDLRVLDNDALYKAWSSSDTILPVYCLDPRLFHTTHFFNFPKTGALRGGFLMECLVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGARTVFAHKETCSEEVDVERLVNQGLKRVGNSTKLELIWGSTMYHKDDLPFDVFDLPDVYTQFRKSVEAKCSIRSSTRIPLSLGPTPSVDDWGDVPTLEKLGVEPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKETRNGMLGPDYSTKFSPWLAFGCISPRFIYEEVQRYEKERVANNSTYWVLFELIWRDYFRFLSIKCGNSLFHLGGPRNVQGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYGAGVGNDPREDRYFSIPKQAQNYDPEGEYVAFWLQQLRRLPKEKRHWPGRLMYMDTVVPLKHGNGP 500
                                    11        21        31        41        51        61        71        81        91       101       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       461       471       481       491

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 2J4D)

(no "CATH Domain" information available for 2J4D)

(no "Pfam Domain" information available for 2J4D)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CRYD_ARATH | Q84KJ5)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003913	DNA photolyase activity	Catalysis of the repair of a photoproduct resulting from ultraviolet irradiation of two adjacent pyrimidine residues in DNA.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0009881	photoreceptor activity	The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation.
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:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
	GO:0050896	response to stimulus	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 stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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		Val B:7 - Pro B:8	[ RasMol ]

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	2j4d
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