3P56 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THE STRUCTURE OF THE HUMAN RNASE H2 COMPLEX DEFINES KEY INTERACTION INTERFACES RELEVANT TO ENZYME FUNCTION AND HUMAN DISEASE

Authors :   D. Bubeck, S. C. Graham, E. Y. Jones

Date :   08 Oct 10 (Deposition) - 17 Nov 10 (Release) - 13 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   4.06

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

Keywords :   Rnase H Fold, Triple Beta-Barrel, Nuclease That Cleaves Rna/Dna Hybrids, Proliferating Cell Nuclear Antigen (Pcna) And Rna/Dna Hybrids, Nucleus, Hydrolase-Replication Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Reijns, D. Bubeck, L. C. Gibson, S. C. Graham, G. S. Baillie, E. Y. Jones, A. P. Jackson
The Structure Of The Human Rnase H2 Complex Defines Key Interaction Interfaces Relevant To Enzyme Function And Huma Disease.
J. Biol. Chem. V. 286 10530 2011
PubMed-ID: 21177854 | Reference-DOI: 10.1074/JBC.M110.177394

Molecule 1 - RIBONUCLEASE H2 SUBUNIT A
	Chains	:	A, D
	EC Number	:	3.1.26.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	POLYCISTRONIC CONSTRUCT BASED ON PGEX6P1
	Expression System Strain	:	ROSETTA-2
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	RNASEH2A, RNASEHI, RNHIA
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RNASE H2 SUBUNIT A, AICARDI-GOUTIERES SYNDROME 4 PROTEIN, AGS4, RNASE H(35), RIBONUCLEASE HI LARGE SUBUNIT, RNASE HI LARGE SUBUNIT, RIBONUCLEASE HI SUBUNIT A

Molecule 2 - RIBONUCLEASE H2 SUBUNIT B
	Chains	:	B, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	POLYCISTRONIC CONSTRUCT BASED ON PGEX6P1
	Expression System Strain	:	ROSETTA-2
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	RNASEH2B, UNP RESIDUES 2-226
	Gene	:	DLEU8, RNASEH2B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RNASE H2 SUBUNIT B, AICARDI-GOUTIERES SYNDROME 2 PROTEIN, AGS2, DELETED IN LYMPHOCYTIC LEUKEMIA 8, RIBONUCLEASE HI SUBUNIT B

Molecule 3 - RIBONUCLEASE H2 SUBUNIT C
	Chains	:	C, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	POLYCISTRONIC CONSTRUCT BASED ON PGEX6P1
	Expression System Strain	:	ROSETTA-2
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	AYP1, RNASEH2C
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RNASE H2 SUBUNIT C, AICARDI-GOUTIERES SYNDROME 3 PROTEIN, AGS3, RNASE H1 SMALL SUBUNIT, RIBONUCLEASE HI SUBUNIT C

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3P56)

(no "Site" information available for 3P56)

(no "SS Bond" information available for 3P56)

(no "Cis Peptide Bond" information available for 3P56)

Asymmetric Unit (27, 54)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_027377	G	37	S	RNH2A_HUMAN	Disease (AGS4)	76857106	A/D	G	37	S
02	UniProt	VAR_070619	D	39	Y	RNH2C_HUMAN	Disease (AGS3)	773527127	C/F	D	39	Y
03	UniProt	VAR_070611	P	43	H	RNH2B_HUMAN	Disease (AGS2)	79564863	B/E	P	43	H
04	UniProt	VAR_027280	L	60	R	RNH2B_HUMAN	Disease (AGS2)	75325951	B/E	L	60	R
05	UniProt	VAR_027287	R	69	W	RNH2C_HUMAN	Disease (AGS3)	78635798	C/F	R	69	W
06	UniProt	VAR_070612	W	73	L	RNH2B_HUMAN	Disease (AGS2)	78071087	B/E	W	73	L
07	UniProt	VAR_070620	P	76	L	RNH2C_HUMAN	Disease (AGS3)	76091978	C/F	P	76	L
08	UniProt	VAR_070613	G	83	S	RNH2B_HUMAN	Disease (AGS2)	76158094	B/E	G	83	S
09	UniProt	VAR_027281	H	86	R	RNH2B_HUMAN	Disease (AGS2)	77931005	B/E	H	86	R
10	UniProt	VAR_070624	N	99	D	RNH2A_HUMAN	Polymorphism	---	A/D	N	99	D
11	UniProt	VAR_070625	R	108	W	RNH2A_HUMAN	Disease (AGS4)	76436818	A/D	R	108	W
12	UniProt	VAR_070614	L	138	F	RNH2B_HUMAN	Disease (AGS2)	78705382	B/E	L	138	F
13	UniProt	VAR_070621	P	138	L	RNH2C_HUMAN	Disease (AGS3)	---	C/F	P	138	L
14	UniProt	VAR_027288	K	143	I	RNH2C_HUMAN	Disease (AGS3)	75146158	C/F	K	143	I
15	UniProt	VAR_070622	P	151	S	RNH2C_HUMAN	Disease (AGS3)	78464826	C/F	P	151	S
16	UniProt	VAR_070615	S	159	I	RNH2B_HUMAN	Disease (AGS2)	76219783	B/E	S	159	I
17	UniProt	VAR_027282	K	162	T	RNH2B_HUMAN	Disease (AGS2)	75971463	B/E	K	162	T
18	UniProt	VAR_027283	T	163	I	RNH2B_HUMAN	Disease (AGS2)	79310911	B/E	T	163	I
19	UniProt	VAR_027284	A	177	T	RNH2B_HUMAN	Disease (AGS2)	75184679	B/E	A	177	T
20	UniProt	VAR_070616	V	183	M	RNH2B_HUMAN	Disease (AGS2)	77377571	B/E	V	183	M
21	UniProt	VAR_070626	R	186	W	RNH2A_HUMAN	Disease (AGS4)	77103971	A/D	R	186	W
22	UniProt	VAR_070627	D	205	E	RNH2A_HUMAN	Polymorphism	62619782	A/D	D	205	E
23	UniProt	VAR_027286	Y	219	H	RNH2B_HUMAN	Disease (AGS2)	77391331	B/E	Y	219	H
24	UniProt	VAR_070628	F	230	L	RNH2A_HUMAN	Disease (AGS4)	79767407	A/D	F	230	L
25	UniProt	VAR_070629	R	235	Q	RNH2A_HUMAN	Disease (AGS4)	75718910	A/D	R	235	Q
26	UniProt	VAR_070630	T	240	M	RNH2A_HUMAN	Disease (AGS4)	79843600	A/D	T	240	M
27	UniProt	VAR_070632	R	291	H	RNH2A_HUMAN	Disease (AGS4)	75037667	A/D	R	291	H

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

Biological Unit 1 (27, 27)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_027377	G	37	S	RNH2A_HUMAN	Disease (AGS4)	76857106	A	G	37	S
02	UniProt	VAR_070619	D	39	Y	RNH2C_HUMAN	Disease (AGS3)	773527127	C	D	39	Y
03	UniProt	VAR_070611	P	43	H	RNH2B_HUMAN	Disease (AGS2)	79564863	B	P	43	H
04	UniProt	VAR_027280	L	60	R	RNH2B_HUMAN	Disease (AGS2)	75325951	B	L	60	R
05	UniProt	VAR_027287	R	69	W	RNH2C_HUMAN	Disease (AGS3)	78635798	C	R	69	W
06	UniProt	VAR_070612	W	73	L	RNH2B_HUMAN	Disease (AGS2)	78071087	B	W	73	L
07	UniProt	VAR_070620	P	76	L	RNH2C_HUMAN	Disease (AGS3)	76091978	C	P	76	L
08	UniProt	VAR_070613	G	83	S	RNH2B_HUMAN	Disease (AGS2)	76158094	B	G	83	S
09	UniProt	VAR_027281	H	86	R	RNH2B_HUMAN	Disease (AGS2)	77931005	B	H	86	R
10	UniProt	VAR_070624	N	99	D	RNH2A_HUMAN	Polymorphism	---	A	N	99	D
11	UniProt	VAR_070625	R	108	W	RNH2A_HUMAN	Disease (AGS4)	76436818	A	R	108	W
12	UniProt	VAR_070614	L	138	F	RNH2B_HUMAN	Disease (AGS2)	78705382	B	L	138	F
13	UniProt	VAR_070621	P	138	L	RNH2C_HUMAN	Disease (AGS3)	---	C	P	138	L
14	UniProt	VAR_027288	K	143	I	RNH2C_HUMAN	Disease (AGS3)	75146158	C	K	143	I
15	UniProt	VAR_070622	P	151	S	RNH2C_HUMAN	Disease (AGS3)	78464826	C	P	151	S
16	UniProt	VAR_070615	S	159	I	RNH2B_HUMAN	Disease (AGS2)	76219783	B	S	159	I
17	UniProt	VAR_027282	K	162	T	RNH2B_HUMAN	Disease (AGS2)	75971463	B	K	162	T
18	UniProt	VAR_027283	T	163	I	RNH2B_HUMAN	Disease (AGS2)	79310911	B	T	163	I
19	UniProt	VAR_027284	A	177	T	RNH2B_HUMAN	Disease (AGS2)	75184679	B	A	177	T
20	UniProt	VAR_070616	V	183	M	RNH2B_HUMAN	Disease (AGS2)	77377571	B	V	183	M
21	UniProt	VAR_070626	R	186	W	RNH2A_HUMAN	Disease (AGS4)	77103971	A	R	186	W
22	UniProt	VAR_070627	D	205	E	RNH2A_HUMAN	Polymorphism	62619782	A	D	205	E
23	UniProt	VAR_027286	Y	219	H	RNH2B_HUMAN	Disease (AGS2)	77391331	B	Y	219	H
24	UniProt	VAR_070628	F	230	L	RNH2A_HUMAN	Disease (AGS4)	79767407	A	F	230	L
25	UniProt	VAR_070629	R	235	Q	RNH2A_HUMAN	Disease (AGS4)	75718910	A	R	235	Q
26	UniProt	VAR_070630	T	240	M	RNH2A_HUMAN	Disease (AGS4)	79843600	A	T	240	M
27	UniProt	VAR_070632	R	291	H	RNH2A_HUMAN	Disease (AGS4)	75037667	A	R	291	H

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

Biological Unit 2 (27, 27)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_027377	G	37	S	RNH2A_HUMAN	Disease (AGS4)	76857106	D	G	37	S
02	UniProt	VAR_070619	D	39	Y	RNH2C_HUMAN	Disease (AGS3)	773527127	F	D	39	Y
03	UniProt	VAR_070611	P	43	H	RNH2B_HUMAN	Disease (AGS2)	79564863	E	P	43	H
04	UniProt	VAR_027280	L	60	R	RNH2B_HUMAN	Disease (AGS2)	75325951	E	L	60	R
05	UniProt	VAR_027287	R	69	W	RNH2C_HUMAN	Disease (AGS3)	78635798	F	R	69	W
06	UniProt	VAR_070612	W	73	L	RNH2B_HUMAN	Disease (AGS2)	78071087	E	W	73	L
07	UniProt	VAR_070620	P	76	L	RNH2C_HUMAN	Disease (AGS3)	76091978	F	P	76	L
08	UniProt	VAR_070613	G	83	S	RNH2B_HUMAN	Disease (AGS2)	76158094	E	G	83	S
09	UniProt	VAR_027281	H	86	R	RNH2B_HUMAN	Disease (AGS2)	77931005	E	H	86	R
10	UniProt	VAR_070624	N	99	D	RNH2A_HUMAN	Polymorphism	---	D	N	99	D
11	UniProt	VAR_070625	R	108	W	RNH2A_HUMAN	Disease (AGS4)	76436818	D	R	108	W
12	UniProt	VAR_070614	L	138	F	RNH2B_HUMAN	Disease (AGS2)	78705382	E	L	138	F
13	UniProt	VAR_070621	P	138	L	RNH2C_HUMAN	Disease (AGS3)	---	F	P	138	L
14	UniProt	VAR_027288	K	143	I	RNH2C_HUMAN	Disease (AGS3)	75146158	F	K	143	I
15	UniProt	VAR_070622	P	151	S	RNH2C_HUMAN	Disease (AGS3)	78464826	F	P	151	S
16	UniProt	VAR_070615	S	159	I	RNH2B_HUMAN	Disease (AGS2)	76219783	E	S	159	I
17	UniProt	VAR_027282	K	162	T	RNH2B_HUMAN	Disease (AGS2)	75971463	E	K	162	T
18	UniProt	VAR_027283	T	163	I	RNH2B_HUMAN	Disease (AGS2)	79310911	E	T	163	I
19	UniProt	VAR_027284	A	177	T	RNH2B_HUMAN	Disease (AGS2)	75184679	E	A	177	T
20	UniProt	VAR_070616	V	183	M	RNH2B_HUMAN	Disease (AGS2)	77377571	E	V	183	M
21	UniProt	VAR_070626	R	186	W	RNH2A_HUMAN	Disease (AGS4)	77103971	D	R	186	W
22	UniProt	VAR_070627	D	205	E	RNH2A_HUMAN	Polymorphism	62619782	D	D	205	E
23	UniProt	VAR_027286	Y	219	H	RNH2B_HUMAN	Disease (AGS2)	77391331	E	Y	219	H
24	UniProt	VAR_070628	F	230	L	RNH2A_HUMAN	Disease (AGS4)	79767407	D	F	230	L
25	UniProt	VAR_070629	R	235	Q	RNH2A_HUMAN	Disease (AGS4)	75718910	D	R	235	Q
26	UniProt	VAR_070630	T	240	M	RNH2A_HUMAN	Disease (AGS4)	79843600	D	T	240	M
27	UniProt	VAR_070632	R	291	H	RNH2A_HUMAN	Disease (AGS4)	75037667	D	R	291	H

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

(no "PROSITE Motif" information available for 3P56)

(no "Exon" information available for 3P56)

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:249
 aligned with RNH2A_HUMAN | O75792 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:290
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299
          RNH2A_HUMAN    10 NTGRCRLSSPVPAVCRKEPCVLGVDEAGRGPVLGPMVYAICYCPLPRLADLEALKVADSKTLLESERERLFAKMEDTDFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLIQYALDQGVNVTQVFVDTVGMPETYQARLQQSFPGIEVTVKAKADALYPVVSAASICAKVARDQAVKKWQFVEKLQDLDTDYGSGYPNDPKTKAWLKEHVEPVFGFPQFVRFSWRTAQTILEKEAEDVIWEDSASENQEGLRKITSYFLNEGSQARPRSSHRYFLERGLESATSL 299
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......hhhhhhh.eeeeeeee.........eeeeeeee..hhhhhh.....---..hhhhhhhhhhhhh--...eeee.eehhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh----------........hhhhhhhhhh...............hhhhhhhhhhh...ee....--------------------------hhhhhhhhheee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------S-------------------------------------------------------------D--------W-----------------------------------------------------------------------------W------------------E------------------------L----Q----M--------------------------------------------------H-------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p56 A  10 NTGRCRLSSPVPAVCRKEPCVLGVAEAGRGPVLGPMVYAICYCPLPRLADLEALKVA---TLLESERERLFAKME--DFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLIQYALDQGVNVTQVFVDTVGMPETYQARLQQSFPGIEVTVKAKAAALYPVVSAASICAKVARDQAVKKWQ----------DYGSGYPNDPKTKAWLKEHVEPVFGFPQFVRFSWRTAQTILEKEAEDVIWEDS--------------------------SHRYFLERGLESATSL 299
                                    19        29        39        49        59      |  -|       79    |  |89        99       109       119       129       139       149       159       169       179       189    |    -     | 209       219       229       239       249       | -         -         -    |  289       299
                                                                                   66  70            84 87                                                                                                        194        205                                                 257                        284

Chain B from PDB  Type:PROTEIN  Length:156
 aligned with RNH2B_HUMAN | Q5TBB1 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:215
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     
          RNH2B_HUMAN    12 GARQHVFLVSEYLKDASKKMKNGLMFVKLVNPCSGEGAIYLFNMCLQQLFEVKVFKEKHHSWFINQSVQSGGLLHFATPVDPLFLLLHYLIKADKEGKFQPLDQVVVDNVFPNCILLLKLPGLEKLLHHVTEEKGNPEIDNKKYYKYSKEKTLKWLEKKVNQTVAALKTNNVNVSSRVQSTAFFSGDQASTDKEEDYIRYAHGLISDYIPKELSD 226
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhh...------.eee......-----.eeee....eeeeeeee.....eeee..eeee...eeeeee.hhhhhhhhhhhh...----------------.hhhhhhh...hhhhhh...-----------.....hhhhhhhhhhhhhhhhhhhhhhh...---------------------.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------H----------------R------------L---------S--R---------------------------------------------------F--------------------I--TI-------------T-----M-----------------------------------H------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p56 B  12 GARQHVFLVSEYLKDAS------LMFVKLVNPC-----IYLFNMCLQQLFEVKVFKEKHHSWFINQSVQSGGLLHFATPVDPLFLLLHYLIKADK----------------PNCILLLKLPGLEKLLHHVT-----------KYYKYSKEKTLKWLEKKVNQTVAALKTNNVN---------------------EDYIRYAHGLISDYIPKELSD 226
                                    21      |  -   |    41  |     51        61        71        81        91       101    |    -         - |     131       141|        -  |    161       171       181  |      -         -    |  211       221     
                                           28     35       44    50                                                     106              123                142         154                           184                   206

Chain C from PDB  Type:PROTEIN  Length:116
 aligned with RNH2C_HUMAN | Q8TDP1 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:147
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       
          RNH2C_HUMAN    14 VHLRSATLRDAVPATLHLLPCEVAVDGPAPVGRFFTPAIRQGPEGLEVSFRGRCLRGEEVAVPPGLVGYVMVTEEKKVSMGKPDPLRDSGTDDQEEEPLERDFDRFIGATANFSRFTLWGLETIPGPDAKVRGALTWPSLAAAIHAQ 160
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.ee...eee..ee...ee.hhhhhh....ee....eeeee..eeeeeeeee....eeeeeee.-------------------------------...eeeeee.eeeeeee.......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------Y-----------------------------W------L-------------------------------------------------------------L----I-------S--------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p56 C  14 VHLRSATLRDAVPATLHLLPCEVAVDGPAPVGRFFTPAIRQGPEGLEVSFRGRCLRGEEVAVPPGLVGYVMVT-------------------------------RFIGATANFSRFTLWGLETIPGPDAKVRGALTWPSLAAAIHAQ 160
                                    23        33        43        53        63        73        83  |      -         -         -    |  123       133       143       153       
                                                                                                   86                             118

Chain D from PDB  Type:PROTEIN  Length:225
 aligned with RNH2A_HUMAN | O75792 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:290
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299
          RNH2A_HUMAN    10 NTGRCRLSSPVPAVCRKEPCVLGVDEAGRGPVLGPMVYAICYCPLPRLADLEALKVADSKTLLESERERLFAKMEDTDFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLIQYALDQGVNVTQVFVDTVGMPETYQARLQQSFPGIEVTVKAKADALYPVVSAASICAKVARDQAVKKWQFVEKLQDLDTDYGSGYPNDPKTKAWLKEHVEPVFGFPQFVRFSWRTAQTILEKEAEDVIWEDSASENQEGLRKITSYFLNEGSQARPRSSHRYFLERGLESATSL 299
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------RNase_HII-3p56D01 D:31-241                                                                                                                                                                                         ----------------                          ---------------- Pfam domains (1)
           Pfam domains (2) ---------------------RNase_HII-3p56D02 D:31-241                                                                                                                                                                                         ----------------                          ---------------- Pfam domains (2)
         Sec.struct. author ...ee......hhhhhhh.eeeeeeee.........eeeeeeee..hhhhhh.....---..hhhhhhhhhhhhh--...eeee.eehhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..eeeeee..------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhh----------........hhhhhhhhhh...............hhhhhhhhhhh...ee....--------------------------hhhhhhhhheee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------S-------------------------------------------------------------D--------W-----------------------------------------------------------------------------W------------------E------------------------L----Q----M--------------------------------------------------H-------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p56 D  10 NTGRCRLSSPVPAVCRKEPCVLGVAEAGRGPVLGPMVYAICYCPLPRLADLEALKVA---TLLESERERLFAKME--DFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLIQYALDQGVNVTQVFVDT------------------------KAAALYPVVSAASICAKVARDQAVKKWQ----------DYGSGYPNDPKTKAWLKEHVEPVFGFPQFVRFSWRTAQTILEKEAEDVIWEDS--------------------------SHRYFLERGLESATSL 299
                                    19        29        39        49        59      |  -|       79    |  |89        99       109       119       129       139  |      -         -       169       179       189    |    -     | 209       219       229       239       249       | -         -         -    |  289       299
                                                                                   66  70            84 87                                                    142                      167                        194        205                                                 257                        284

Chain E from PDB  Type:PROTEIN  Length:158
 aligned with RNH2B_HUMAN | Q5TBB1 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:215
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     
          RNH2B_HUMAN    12 GARQHVFLVSEYLKDASKKMKNGLMFVKLVNPCSGEGAIYLFNMCLQQLFEVKVFKEKHHSWFINQSVQSGGLLHFATPVDPLFLLLHYLIKADKEGKFQPLDQVVVDNVFPNCILLLKLPGLEKLLHHVTEEKGNPEIDNKKYYKYSKEKTLKWLEKKVNQTVAALKTNNVNVSSRVQSTAFFSGDQASTDKEEDYIRYAHGLISDYIPKELSD 226
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --RNase_H2-Ydr279     -3p56E01 E:    14-226                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) --RNase_H2-Ydr279     -3p56E02 E:    14-226                                                                                                                                                                             Pfam domains (2)
         Sec.struct. author ...eeeeeee.hhh...-----.eeeee.....----.eeeee....eeeeeeee.....eeee..eeee...eeeeee.hhhhhhhhhhhh...----------------.hhhhhhh...hhhhhh...-----------.....hhhhhhhhhhhhhhhhhhhhhhh...---------------------.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------H----------------R------------L---------S--R---------------------------------------------------F--------------------I--TI-------------T-----M-----------------------------------H------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p56 E  12 GARQHVFLVSEYLKDAS-----GLMFVKLVNPC----AIYLFNMCLQQLFEVKVFKEKHHSWFINQSVQSGGLLHFATPVDPLFLLLHYLIKADK----------------PNCILLLKLPGLEKLLHHVT-----------KYYKYSKEKTLKWLEKKVNQTVAALKTNNVN---------------------EDYIRYAHGLISDYIPKELSD 226
                                    21      |  -  |     41  |    |51        61        71        81        91       101    |    -         - |     131       141|        -  |    161       171       181  |      -         -    |  211       221     
                                           28    34        44   49                                                      106              123                142         154                           184                   206

Chain F from PDB  Type:PROTEIN  Length:116
 aligned with RNH2C_HUMAN | Q8TDP1 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:147
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       
          RNH2C_HUMAN    14 VHLRSATLRDAVPATLHLLPCEVAVDGPAPVGRFFTPAIRQGPEGLEVSFRGRCLRGEEVAVPPGLVGYVMVTEEKKVSMGKPDPLRDSGTDDQEEEPLERDFDRFIGATANFSRFTLWGLETIPGPDAKVRGALTWPSLAAAIHAQ 160
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------RNase_H2_suC-3p56F01 F:28-157                                                                                                     --- Pfam domains (1)
           Pfam domains (2) --------------RNase_H2_suC-3p56F02 F:28-157                                                                                                     --- Pfam domains (2)
         Sec.struct. author .ee.hhhhhh.ee...eee..ee...ee.hhhhhh....ee....eeeee..eeeeeeeee....eeeeeee.-------------------------------...eeeeee.eeeeeee.......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------Y-----------------------------W------L-------------------------------------------------------------L----I-------S--------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p56 F  14 VHLRSATLRDAVPATLHLLPCEVAVDGPAPVGRFFTPAIRQGPEGLEVSFRGRCLRGEEVAVPPGLVGYVMVT-------------------------------RFIGATANFSRFTLWGLETIPGPDAKVRGALTWPSLAAAIHAQ 160
                                    23        33        43        53        63        73        83  |      -         -         -    |  123       133       143       153       
                                                                                                   86                             118

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 3P56)

(no "CATH Domain" information available for 3P56)

Asymmetric Unit(hide GO term definitions)

Chain A,D (RNH2A_HUMAN | O75792)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004523	RNA-DNA hybrid ribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0004540	ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0043137	DNA replication, removal of RNA primer	Removal of the Okazaki RNA primer from the lagging strand of replicating DNA, by a combination of the actions of DNA polymerase, DNA helicase and an endonuclease.
	GO:0006401	RNA catabolic process	The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0016070	RNA metabolic process	The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0006298	mismatch repair	A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.
	GO:0032299	ribonuclease H2 complex	A protein complex that possesses ribonuclease H activity, in which the catalytic subunit is a member of the RNase H2 (or HII) class. For example, in Saccharomyces the complex contains Rnh201p, Rnh202p and Rnh203p.

Chain B,E (RNH2B_HUMAN | Q5TBB1)

molecular function
	GO:0004523	RNA-DNA hybrid ribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
biological process
	GO:0006401	RNA catabolic process	The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0001701	in utero embryonic development	The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
	GO:0010629	negative regulation of gene expression	Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0048146	positive regulation of fibroblast proliferation	Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
	GO:2000001	regulation of DNA damage checkpoint	Any process that modulates the frequency, rate or extent of a DNA damage checkpoint.
	GO:0010389	regulation of G2/M transition of mitotic cell cycle	Any process that modulates the rate or extent of progression from G2 phase to M phase of the mitotic cell cycle.
	GO:0009259	ribonucleotide metabolic process	The chemical reactions and pathways involving a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
	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.
	GO:0032299	ribonuclease H2 complex	A protein complex that possesses ribonuclease H activity, in which the catalytic subunit is a member of the RNase H2 (or HII) class. For example, in Saccharomyces the complex contains Rnh201p, Rnh202p and Rnh203p.

Chain C,F (RNH2C_HUMAN | Q8TDP1)

molecular function
	GO:0004523	RNA-DNA hybrid ribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
biological process
	GO:0006401	RNA catabolic process	The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
cellular component
	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.
	GO:0032299	ribonuclease H2 complex	A protein complex that possesses ribonuclease H activity, in which the catalytic subunit is a member of the RNase H2 (or HII) class. For example, in Saccharomyces the complex contains Rnh201p, Rnh202p and Rnh203p.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3p56)

	Sites
(no "Sites" information available for 3p56)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3p56)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3p56
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RNH2A_HUMAN \| O75792
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	RNH2B_HUMAN \| Q5TBB1
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	RNH2C_HUMAN \| Q8TDP1
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.1.26.4
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	610181
		Disease Information	:	OMIM
	610329
		Disease Information	:	OMIM
	610333
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RNH2A_HUMAN \| O75792
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	RNH2B_HUMAN \| Q5TBB1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	RNH2C_HUMAN \| Q8TDP1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	RNH2A_HUMAN \| O75792	:	3puf
	RNH2B_HUMAN \| Q5TBB1	:	3p87 3puf
	RNH2C_HUMAN \| Q8TDP1	:	3puf

3kio	MURINE RNASE H2
3p5j	MURINE RNASE H2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (27, 54)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (3, 6)

Gene Ontology (26, 36)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File