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Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HUMAN SNP PAD4 PROTEIN

Authors :   N. Horikoshi, H. Tachiwana, K. Saito, A. Osakabe, M. Sato, M. Yamada, S. Y. Nishimura, W. Kagawa, H. Kurumizaka

Date :   19 Oct 10 (Deposition) - 26 Jan 11 (Release) - 11 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Alpha/Beta-Propeller, Immunoglobulin-Like, Arginine Citrullination, Hydrolase, Protein-Arginine Deiminase, Post-Translational Modification, Calcium Binding, Histone Binding, Benzoyl-L-Arginine Amide Binding, Nucleus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Horikoshi, H. Tachiwana, K. Saito, A. Osakabe, M. Sato, M. Yamada, S. Akashi, Y. Nishimura, W. Kagawa, H. Kurumizaka
Structural And Biochemical Analyses Of The Human Pad4 Variant Encoded By A Functional Haplotype Gene
Acta Crystallogr. , Sect. D V. 67 112 2011
PubMed-ID: 21245532 | Reference-DOI: 10.1107/S0907444910051711

Molecule 1 - PROTEIN-ARGININE DEIMINASE TYPE-4
	Chains	:	A
	EC Number	:	3.5.3.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PADI4, PADI5, PDI5
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PAD4, HL-60 PAD, PEPTIDYLARGININE DEIMINASE IV, PROTEIN- ARGININE DEIMINASE TYPE IV

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

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 3APM)

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

(no "Cis Peptide Bond" information available for 3APM)

Asymmetric Unit (8, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_053560	R	8	H	PADI4_HUMAN	Polymorphism	35381732	A	R	8	H
2	UniProt	VAR_053561	T	79	M	PADI4_HUMAN	Polymorphism	35809521	A	T	79	M
3	UniProt	VAR_020640	V	82	A	PADI4_HUMAN	Polymorphism	11203367	A	V	82	A
4	UniProt	VAR_027401	D	89	N	PADI4_HUMAN	Polymorphism	143187209	A	D	89	N
5	UniProt	VAR_027402	P	102	T	PADI4_HUMAN	Polymorphism	34309058	A	P	102	T
6	UniProt	VAR_020641	G	112	A	PADI4_HUMAN	Polymorphism	874881	A	G	112	A
7	UniProt	VAR_053562	D	260	N	PADI4_HUMAN	Polymorphism	35903413	A	D	260	N
8	UniProt	VAR_020642	S	275	F	PADI4_HUMAN	Polymorphism	1748020	A	S	275	F

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

Biological Unit 1 (8, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_053560	R	8	H	PADI4_HUMAN	Polymorphism	35381732	A	R	8	H
2	UniProt	VAR_053561	T	79	M	PADI4_HUMAN	Polymorphism	35809521	A	T	79	M
3	UniProt	VAR_020640	V	82	A	PADI4_HUMAN	Polymorphism	11203367	A	V	82	A
4	UniProt	VAR_027401	D	89	N	PADI4_HUMAN	Polymorphism	143187209	A	D	89	N
5	UniProt	VAR_027402	P	102	T	PADI4_HUMAN	Polymorphism	34309058	A	P	102	T
6	UniProt	VAR_020641	G	112	A	PADI4_HUMAN	Polymorphism	874881	A	G	112	A
7	UniProt	VAR_053562	D	260	N	PADI4_HUMAN	Polymorphism	35903413	A	D	260	N
8	UniProt	VAR_020642	S	275	F	PADI4_HUMAN	Polymorphism	1748020	A	S	275	F

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

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

Asymmetric Unit (16, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000375448	1b	ENSE00001883200	chr1:17634692-17634809	118	PADI4_HUMAN	1-31	31	1	A:2-31	30
1.2	ENST00000375448	2	ENSE00001268578	chr1:17657464-17657644	181	PADI4_HUMAN	31-91	61	1	A:31-91 (gaps)	61
1.3	ENST00000375448	3	ENSE00001044965	chr1:17660438-17660504	67	PADI4_HUMAN	92-114	23	1	A:92-114	23
1.6	ENST00000375448	6	ENSE00001044983	chr1:17662654-17662721	68	PADI4_HUMAN	114-136	23	1	A:114-136 (gaps)	23
1.7	ENST00000375448	7	ENSE00001044981	chr1:17664533-17664650	118	PADI4_HUMAN	137-176	40	1	A:137-176 (gaps)	40
1.8	ENST00000375448	8	ENSE00001044989	chr1:17666183-17666308	126	PADI4_HUMAN	176-218	43	1	A:176-218	43
1.9	ENST00000375448	9	ENSE00001268541	chr1:17668438-17668616	179	PADI4_HUMAN	218-277	60	1	A:218-277 (gaps)	60
1.10	ENST00000375448	10	ENSE00001044974	chr1:17668794-17668897	104	PADI4_HUMAN	278-312	35	1	A:278-312	35
1.11a	ENST00000375448	11a	ENSE00001044969	chr1:17672523-17672634	112	PADI4_HUMAN	312-349	38	1	A:312-349 (gaps)	38
1.12b	ENST00000375448	12b	ENSE00001044980	chr1:17674436-17674543	108	PADI4_HUMAN	350-385	36	1	A:350-370	21
1.14	ENST00000375448	14	ENSE00001044967	chr1:17681028-17681182	155	PADI4_HUMAN	386-437	52	1	A:388-437 (gaps)	50
1.15	ENST00000375448	15	ENSE00001044986	chr1:17682478-17682622	145	PADI4_HUMAN	437-485	49	1	A:437-485	49
1.16b	ENST00000375448	16b	ENSE00001044971	chr1:17682852-17682954	103	PADI4_HUMAN	486-520	35	1	A:486-515	30
1.17b	ENST00000375448	17b	ENSE00001044973	chr1:17685333-17685403	71	PADI4_HUMAN	520-543	24	1	A:522-543	22
1.18	ENST00000375448	18	ENSE00001044963	chr1:17685775-17685903	129	PADI4_HUMAN	544-586	43	1	A:544-586	43
1.19	ENST00000375448	19	ENSE00001467124	chr1:17690017-17690499	483	PADI4_HUMAN	587-663	77	1	A:587-663 (gaps)	77

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:559
 aligned with PADI4_HUMAN | Q9UM07 from UniProtKB/Swiss-Prot  Length:663

    Alignment length:662
                                    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       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661  
          PADI4_HUMAN     2 AQGTLIRVTPEQPTHAVCVLGTLTQLDICSSAPEDCTSFSINASPGVVVDIAHGPPAKKKSTGSSTWPLDPGVEVTLTMKVASGSTGDQKVQISYYGPKTPPVKALLYLTGVEISLCADITRTGKVKPTRAVKDQRTWTWGPCGQGAILLVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDKVRVFQATRGKLSSKCSVVLGPKWPSHYLMVPGGKHNMDFYVEALAFPDTDFPGLITLTISLLDTSNLELPEAVVFQDSVVFRVAPWIMTPNTQPPQEVYACSIFENEDFLKSVTTLAMKAKCKLTICPEEENMDDQWMQDEMEIGYIQAPHKTLPVVFDSPRNRGLKEFPIKRVMGPDFGYVTRGPQTGGISGLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHGEALLFEGIKKKKQQKIKNILSNKTLREHNSFVERCIDWNRELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPNMVNMLVLGKHLGIPKPFGPVINGRCCLEEKVCSLLEPLGLQCTFINDFFTYHIRHGEVHCGTNVRRKPFSFKWWNMVP 663
               SCOP domains d3apma1 A:2-112 Peptidylarginin      e deiminase Pad4           , N-terminal domain                            d3apma2 A:113-29       3 Peptidylarginine dei              minase Pad4, middle domain                                                                                                d3apma3 A:294-663 P       eptidylarginine de           iminase Pad4, catalyti                 c C-term       inal domain                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee......eeeeee....eeee....------.eeeee......eee.-----------.........eeee...........eeeeeeeee..eeeeeeeeeeeeeeeeee..........-------.............ee.......--------------.hhhhh...eeeeeeeee..hhhh.eeeeee....hhh.eeeeee..-----.eeeee.....eee.....eeeeeeeeeee..........eeeeeeeeee........eeeeeeeeeeee...........eeeeee..-------..hhhhhhhhhh.eeee.-----------....eeeeeee..eeeeeee..-----------------..eee...-------...hhh.eee...eee..eee....eeeee...........hhhhhhhhhhhh....eeee.......hhhh.eeeee......eeeeeeehhhhhhhhhhhhhh.....ee.------..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeee..eee.hhh.eee........eee..eeeee.....ee..eehhhhhhhhhhhhhh.eeeee..------------..eeeee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------H----------------------------------------------------------------------M--A------N------------T---------A---------------------------------------------------------------------------------------------------------------------------------------------------N--------------F---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:2-31        ------------------------------------------------------------Exon 1.3  PDB: A:92-114----------------------Exon 1.7  PDB: A:137-176 (gaps)         -----------------------------------------Exon 1.9  PDB: A:218-277 (gaps) UniProt: 218-277            Exon 1.10  PDB: A:278-312          -------------------------------------Exon 1.12b  PDB: A:350-370          Exon 1.14  PDB: A:388-437 (gaps) UniProt: 386-437   ------------------------------------------------Exon 1.16b  PDB: A:486-515         -----------------------Exon 1.18  PDB: A:544-586 UniProt: 544-586 Exon 1.19  PDB: A:587-663 (gaps) UniProt: 587-663                             Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.2  PDB: A:31-91 (gaps) UniProt: 31-91                 ----------------------Exon 1.6               ---------------------------------------Exon 1.8  PDB: A:176-218 UniProt: 176-218  ---------------------------------------------------------------------------------------------Exon 1.11a  PDB: A:312-349 (gaps)     ---------------------------------------------------------------------------------------Exon 1.15  PDB: A:437-485 UniProt: 437-485       ----------------------------------Exon 1.17b [INCOMPLETE] ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3apm A   2 AQGTLIRVTPEQPTHAVCVLGTLTQLDICSS------SFSINASPGVVVDIAH-----------STWPLDPGVEVTLTMKVASGSTGDQKVQISYYGPKTPPVKALLYLTGVEISLCADITRTGKVK-------QRTWTWGPCGQGAILLVNCDRD--------------LDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDKVRVFQATR-----KCSVVLGPKWPSHYLMVPGGKHNMDFYVEALAFPDTDFPGLITLTISLLDTSNLELPEAVVFQDSVVFRVAPWIMTPNTQPPQEVYACS-------LKSVTTLAMKAKCKLTIC-----------QDEMEIGYIQAPHKTLPVVFDS-----------------DFGYVTRG-------GLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHGEALLF------KQQKIKNILSNKTLREHNSFVERCIDWNRELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPNMVNMLVLGKHLGIPKPFGPVINGRCCLEEKVCSLLEPLGLQCTFIND------------CGTNVRRKPFSFKWWNMVP 663
                                    11        21        31|      |41        51  |      -    |   71        81        91       101       111       121      |  -    |  141       151     |   -         -|      181       191       201       211      |  -  |    231       241       251       261       271       281       291       301       311|      321       331     |   -       351       361        |-         -      |391   |     - |     411       421       431       441       451       461       471       481       491       501       511   |     -|      531       541       551       561       571       581       591       601       611       621       631|        -   |   651       661  
                                                         32     39             54          66                                                           128     136                  157            172                                           218   224                                                                                     312     320              337         349                  370               388    395     403                                                                                                             515    522                                                                                                           632          645

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 "CATH Domain" information available for 3APM)

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

Asymmetric Unit(hide GO term definitions)

Chain A (PADI4_HUMAN | Q9UM07)

molecular function
	GO:0016990	arginine deiminase activity	Catalysis of the reaction: L-arginine + H2O = L-citrulline + NH3.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004668	protein-arginine deiminase activity	Catalysis of the reaction: protein L-arginine + H2O = protein L-citrulline + NH3.
biological process
	GO:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
	GO:0006325	chromatin organization	Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
	GO:0006338	chromatin remodeling	Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
	GO:0036413	histone H3-R26 citrullination	The hydrolysis of peptidyl-arginine to form peptidyl-citrulline at position 26 in histone H3.
	GO:0036414	histone citrullination	The hydrolysis of peptidyl-arginine to form peptidyl-citrulline on a histone protein.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006334	nucleosome assembly	The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
	GO:0018101	protein citrullination	The hydrolysis of peptidyl-arginine to form peptidyl-citrulline.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0019827	stem cell population maintenance	The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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