1ZBU - JenaLib

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Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FULL-LENGTH 3'-EXONUCLEASE

Authors :   Y. Cheng, D. J. Patel

Date :   08 Apr 05 (Deposition) - 19 Sep 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   3'-Exonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Cheng, D. J. Patel
Structural Basis For 3'-End Specific Recognition Of Histone Mrna Stem-Loop By 3'-Exonuclease, A Human Nuclease That Als Targets Sirna
To Be Published
PubMed: search

Molecule 1 - 3'-5' EXONUCLEASE ERI1
	Chains	:	A, B, C, D
	EC Number	:	3.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ERI1, 3'EXO
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ERI-1 HOMOLOG; HISTONE MRNA 3' END-SPECIFIC EXORIBONUCLEASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 46)

No.	Name	Count	Type	Full Name
1	AMP	4	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	MG	8	Ligand/Ion	MAGNESIUM ION
3	MSE	34	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 11)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (2, 9)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (2, 9)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:134 , ASP A:234 , MG A:1001 , AMP A:1002	BINDING SITE FOR RESIDUE MG A 1000
02	AC2	SOFTWARE	ASP A:134 , PHE A:135 , GLU A:136 , ASP A:298 , MG A:1000 , AMP A:1002	BINDING SITE FOR RESIDUE MG A 1001
03	AC3	SOFTWARE	ASP B:134 , PHE B:135 , ASP B:234 , MG B:2001 , AMP B:2002	BINDING SITE FOR RESIDUE MG B 2000
04	AC4	SOFTWARE	ASP B:134 , GLU B:136 , ASP B:298 , MG B:2000 , AMP B:2002	BINDING SITE FOR RESIDUE MG B 2001
05	AC5	SOFTWARE	ASP C:134 , PHE C:135 , ASP C:234 , AMP C:3002	BINDING SITE FOR RESIDUE MG C 3000
06	AC6	SOFTWARE	ASP C:134 , GLU C:136 , ASP C:298 , AMP C:3002	BINDING SITE FOR RESIDUE MG C 3001
07	AC7	SOFTWARE	ASP D:134 , ASP D:230 , TRP D:233 , ASP D:234 , MG D:4001 , AMP D:4002	BINDING SITE FOR RESIDUE MG D 4000
08	AC8	SOFTWARE	ASP D:134 , PHE D:135 , ASP D:234 , MG D:4000 , AMP D:4002	BINDING SITE FOR RESIDUE MG D 4001
09	AC9	SOFTWARE	ASP A:134 , PHE A:135 , GLU A:136 , ALA A:137 , THR A:138 , CYS A:139 , ASN A:143 , PHE A:185 , PHE A:238 , HIS A:293 , MG A:1000 , MG A:1001	BINDING SITE FOR RESIDUE AMP A 1002
10	BC1	SOFTWARE	ASP B:134 , PHE B:135 , GLU B:136 , ALA B:137 , THR B:138 , CYS B:139 , ASN B:143 , PHE B:185 , PHE B:238 , HIS B:293 , MG B:2000 , MG B:2001	BINDING SITE FOR RESIDUE AMP B 2002
11	BC2	SOFTWARE	ASP C:134 , PHE C:135 , GLU C:136 , ALA C:137 , THR C:138 , CYS C:139 , ASN C:143 , PHE C:185 , PHE C:238 , HIS C:293 , MG C:3000 , MG C:3001	BINDING SITE FOR RESIDUE AMP C 3002
12	BC3	SOFTWARE	PHE D:135 , GLU D:136 , ALA D:137 , THR D:138 , CYS D:139 , ASN D:143 , PHE D:185 , THR D:190 , TRP D:233 , PHE D:238 , HIS D:293 , MG D:4000 , MG D:4001	BINDING SITE FOR RESIDUE AMP D 4002

(no "SS Bond" information available for 1ZBU)

(no "Cis Peptide Bond" information available for 1ZBU)

(no "SAP(SNP)/Variant" information available for 1ZBU)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAP	PS50800	SAP motif profile.	ERI1_HUMAN	76-110	1	B:76-110

Biological Unit 1 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAP	PS50800	SAP motif profile.	ERI1_HUMAN	76-110	0	-

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAP	PS50800	SAP motif profile.	ERI1_HUMAN	76-110	1	B:76-110

Biological Unit 3 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAP	PS50800	SAP motif profile.	ERI1_HUMAN	76-110	0	-

Biological Unit 4 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAP	PS50800	SAP motif profile.	ERI1_HUMAN	76-110	0	-

Asymmetric Unit (6, 21)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000250263	2b	ENSE00001019501	chr8:8860314-8860681	368	ERI1_HUMAN	1-36	36	0	-	-
1.4b	ENST00000250263	4b	ENSE00001019499	chr8:8865480-8865658	179	ERI1_HUMAN	37-96	60	1	- B:41-96 (gaps) - -	- 56 - -
1.6a	ENST00000250263	6a	ENSE00001019497	chr8:8869052-8869262	211	ERI1_HUMAN	96-166	71	4	A:125-166 B:96-166 C:125-166 D:125-166	42 71 42 42
1.7a	ENST00000250263	7a	ENSE00001019504	chr8:8873832-8873915	84	ERI1_HUMAN	167-194	28	4	A:167-194 B:167-194 C:167-194 D:167-194	28 28 28 28
1.8b	ENST00000250263	8b	ENSE00000924781	chr8:8875807-8875916	110	ERI1_HUMAN	195-231	37	4	A:195-231 B:195-231 C:195-231 D:195-231	37 37 37 37
1.9a	ENST00000250263	9a	ENSE00000924782	chr8:8877860-8877974	115	ERI1_HUMAN	231-269	39	4	A:231-269 B:231-269 C:231-269 D:231-269	39 39 39 39
1.10b	ENST00000250263	10b	ENSE00001533120	chr8:8887302-8890848	3547	ERI1_HUMAN	270-349	80	4	A:270-349 B:270-349 C:270-349 D:270-349	80 80 80 80

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:225
 aligned with ERI1_HUMAN | Q8IV48 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:225
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344     
           ERI1_HUMAN   125 SYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDWMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGRPHCGLDDSKNIARIAVRMLQDGCELRINEKMHAGQLMSVSSSLPIEGTPPPQMPHFRK 349
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1zbuA01 A:125-321  [code=3.30.420.10, no name defined]                                                                                                                                               ---------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...ee.............eee..eeeee.....eeeee...ee.......hhhhhhhhh.hhhhhhh.eehhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh....hhhh.eeeehhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh.......eeee..eeee.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) ------------------------------------------Exon 1.7a  PDB: A:167-194   Exon 1.8b  PDB: A:195-231            --------------------------------------Exon 1.10b  PDB: A:270-349 UniProt: 270-349                                      Transcript 1 (1)
           Transcript 1 (2) Exon 1.6a  PDB: A:125-166 UniProt: 96-166 ----------------------------------------------------------------Exon 1.9a  PDB: A:231-269              -------------------------------------------------------------------------------- Transcript 1 (2)
                 1zbu A 125 SYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDLmKLKELGTKYKYSLLTDGSWDmSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTImLEKLGmDYDGRPHCGLDDSKNIARIAVRmLQDGCELRINEKmHAGQLmSVSSSLPIEGTPPPQmPHFRK 349
                                   134       144       154       164       174       184       194       204       214       224       234|      244       254       264       274     | 284 |     294       304    |  314       324   |   334       344     
                                                                                                                   214-MSE              235-MSE                                      280-MSE |                    309-MSE      322-MSE |             344-MSE 
                                                                                                                                                                                           286-MSE                                   328-MSE

Chain B from PDB  Type:PROTEIN  Length:304
 aligned with ERI1_HUMAN | Q8IV48 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:309
                                    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         
           ERI1_HUMAN    41 CKFDGQETKGSKFITSSASDFSDPVYKEIAITNGCINRMSKEELRAKLSEFKLETRGVKDVLKKRLKNYYKKQKLMLKESNFADSYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDWMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGRPHCGLDDSKNIARIAVRMLQDGCELRINEKMHAGQLMSVSSSLPIEGTPPPQMPHFRK 349
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------1zbuB02 B:125-349  [code=3.30.420.10, no name defined]                                                                                                                                                                            CATH domains
               Pfam domains -----------------------------------SAP-1zbuB01 B:76-110               ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..eeeee...-----hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.eeeee.........eeee...ee.............eeeeeeeeee.....eeeeeeee.........hhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh....hhhh.eeeehhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh.......eee....eee.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------SAP  PDB: B:76-110 UniProt: 76-110 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4b  PDB: B:41-96 (gaps) UniProt: 37-96           ----------------------------------------------------------------------Exon 1.7a  PDB: B:167-194   Exon 1.8b  PDB: B:195-231            --------------------------------------Exon 1.10b  PDB: B:270-349 UniProt: 270-349                                      Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.6a  PDB: B:96-166 UniProt: 96-166                               ----------------------------------------------------------------Exon 1.9a  PDB: B:231-269              -------------------------------------------------------------------------------- Transcript 1 (2)
                 1zbu B  41 CKFDGQETKGSKFITSSASD-----YKEIAITNGCINRmSKEELRAKLSEFKLETRGVKDVLKKRLKNYYKKQKLmLKESNFADSYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDLmKLKELGTKYKYSLLTDGSWDmSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTImLEKLGmDYDGRPHCGLDDSKNIARIAVRmLQDGCELRINEKmHAGQLmSVSSSLPIEGTPPPQmPHFRK 349
                                    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   |     
                                              60    66           79-MSE                              116-MSE                                                                                           214-MSE              235-MSE                                      280-MSE |                    309-MSE      322-MSE |             344-MSE 
                                                                                                                                                                                                                                                                               286-MSE                                   328-MSE

Chain C from PDB  Type:PROTEIN  Length:225
 aligned with ERI1_HUMAN | Q8IV48 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:225
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344     
           ERI1_HUMAN   125 SYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDWMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGRPHCGLDDSKNIARIAVRMLQDGCELRINEKMHAGQLMSVSSSLPIEGTPPPQMPHFRK 349
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1zbuC01 C:125-321  [code=3.30.420.10, no name defined]                                                                                                                                               ---------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...ee.............eeeeeeeeee.....eeeeeeee.........hhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh....hhhh.eeeehhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh.......eeee..eeee.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) ------------------------------------------Exon 1.7a  PDB: C:167-194   Exon 1.8b  PDB: C:195-231            --------------------------------------Exon 1.10b  PDB: C:270-349 UniProt: 270-349                                      Transcript 1 (1)
           Transcript 1 (2) Exon 1.6a  PDB: C:125-166 UniProt: 96-166 ----------------------------------------------------------------Exon 1.9a  PDB: C:231-269              -------------------------------------------------------------------------------- Transcript 1 (2)
                 1zbu C 125 SYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDLmKLKELGTKYKYSLLTDGSWDmSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTImLEKLGmDYDGRPHCGLDDSKNIARIAVRmLQDGCELRINEKmHAGQLmSVSSSLPIEGTPPPQmPHFRK 349
                                   134       144       154       164       174       184       194       204       214       224       234|      244       254       264       274     | 284 |     294       304    |  314       324   |   334       344     
                                                                                                                   214-MSE              235-MSE                                      280-MSE |                    309-MSE      322-MSE |             344-MSE 
                                                                                                                                                                                           286-MSE                                   328-MSE

Chain D from PDB  Type:PROTEIN  Length:225
 aligned with ERI1_HUMAN | Q8IV48 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:225
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344     
           ERI1_HUMAN   125 SYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDWMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGRPHCGLDDSKNIARIAVRMLQDGCELRINEKMHAGQLMSVSSSLPIEGTPPPQMPHFRK 349
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1zbuD01 D:125-321  [code=3.30.420.10, no name defined]                                                                                                                                               ---------------------------- CATH domains
           Pfam domains (1) ------RNase_T-1zbuD01 D:131-306                                                                                                                                                       ------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------RNase_T-1zbuD02 D:131-306                                                                                                                                                       ------------------------------------------- Pfam domains (2)
           Pfam domains (3) ------RNase_T-1zbuD03 D:131-306                                                                                                                                                       ------------------------------------------- Pfam domains (3)
           Pfam domains (4) ------RNase_T-1zbuD04 D:131-306                                                                                                                                                       ------------------------------------------- Pfam domains (4)
         Sec.struct. author ....eeeee..ee.............eee..eeeee.....eeeee............hhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh....hhhh.eeeehhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.......eee....eee.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) ------------------------------------------Exon 1.7a  PDB: D:167-194   Exon 1.8b  PDB: D:195-231            --------------------------------------Exon 1.10b  PDB: D:270-349 UniProt: 270-349                                      Transcript 1 (1)
           Transcript 1 (2) Exon 1.6a  PDB: D:125-166 UniProt: 96-166 ----------------------------------------------------------------Exon 1.9a  PDB: D:231-269              -------------------------------------------------------------------------------- Transcript 1 (2)
                 1zbu D 125 SYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDLmKLKELGTKYKYSLLTDGSWDmSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTImLEKLGmDYDGRPHCGLDDSKNIARIAVRmLQDGCELRINEKmHAGQLmSVSSSLPIEGTPPPQmPHFRK 349
                                   134       144       154       164       174       184       194       204       214       224       234|      244       254       264       274     | 284 |     294       304    |  314       324   |   334       344     
                                                                                                                   214-MSE              235-MSE                                      280-MSE |                    309-MSE      322-MSE |             344-MSE 
                                                                                                                                                                                           286-MSE                                   328-MSE

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 1ZBU)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Nucleotidyltransferase; domain 5 (788)

Homologous Superfamily: [code=3.30.420.10, no name defined] (372)

Human (Homo sapiens) (2)

1a	1zbuA01	A:125-321
1b	1zbuC01	C:125-321
1c	1zbuD01	D:125-321
1d	1zbuB02	B:125-349

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HeH (20)

Family: SAP (10)

Homo sapiens (Human) (7)

SAP-1zbuB01

B:76-110

Clan: RNase_H (288)

Family: RNase_T (14)

Homo sapiens (Human) (6)

2a	RNase_T-1zbuD01	D:131-306
2b	RNase_T-1zbuD02	D:131-306
2c	RNase_T-1zbuD03	D:131-306
2d	RNase_T-1zbuD04	D:131-306

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ERI1_HUMAN | Q8IV48)

molecular function
	GO:0008408	3'-5' exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004527	exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
	GO:0071207	histone pre-mRNA stem-loop binding	Interacting selectively and non-covalently with a conserved stem-loop structure found in histone pre-mRNAs.
	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:0019843	rRNA binding	Interacting selectively and non-covalently with ribosomal RNA.
	GO:0043022	ribosome binding	Interacting selectively and non-covalently with any part of a ribosome.
biological process
	GO:0000467	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	Exonucleolytic digestion of a pre-rRNA molecule to generate the mature 3'-end of a 5.8S rRNA molecule derived from an originally tricistronic pre-rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript.
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	GO:0071044	histone mRNA catabolic process	The chemical reactions and pathways resulting in the breakdown of histone messenger RNA (mRNA).
	GO:0031125	rRNA 3'-end processing	Any process involved in forming the mature 3' end of an rRNA molecule.
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0071204	histone pre-mRNA 3'end processing complex	A ribonucleoprotein that binds to specific sites in, and is required for cleavage of, the 3'-end of histone pre-mRNAs. The complex contains the U7 snRNP and additional proteins, including the stem-loop binding protein (SLBP) and the exonuclease 3'hExo/Eri-1.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
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	1zbu
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	3.1.-.-
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UniProtKB/Swiss-Prot
	ERI1_HUMAN \| Q8IV48	:	1w0h 1zbh 4l8r 4qoz

1w0h	HIGH RESOLUTION STRUCTURE OF NUCLEASE DOMAIN
1zbh	COMPLEX STRUCTURE OF 3'HEXO WITH SL-RNA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 46)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (6, 21)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 4)

Pfam Domains (2, 5)

Gene Ontology (19, 19)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File