4F7U - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THE 6S SNRNP ASSEMBLY INTERMEDIATE

Authors :   C. Grimm, J. P. Pelz

Date :   16 May 12 (Deposition) - 30 Jan 13 (Release) - 28 Jan 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J,P,Q
Biol. Unit 1: A,B,E,F,G,P  (1x)
Biol. Unit 2: C,D,H,I,J,Q  (1x)

Keywords :   Assembly Machine, Splicing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Grimm, A. Chari, J. P. Pelz, J. Kuper, C. Kisker, K. Diederichs, H. Stark, H. Schindelin, U. Fischer
Structural Basis Of Assembly Chaperone- Mediated Snrnp Formation.
Mol. Cell V. 49 692 2013
PubMed-ID: 23333303 | Reference-DOI: 10.1016/J.MOLCEL.2012.12.009

Molecule 1 - SMALL NUCLEAR RIBONUCLEOPROTEIN SM D1
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	SNRPD1
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	SM-D1, SM-D AUTOANTIGEN, SNRNP CORE PROTEIN D1

Molecule 2 - SMALL NUCLEAR RIBONUCLEOPROTEIN SM D2
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	SNRPD2
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	SM-D2, SNRNP CORE PROTEIN D2

Molecule 3 - SMALL NUCLEAR RIBONUCLEOPROTEIN E
	Chains	:	E, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	SNRPE
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	SNRNP-E, SM PROTEIN E, SM-E, SME

Molecule 4 - SMALL NUCLEAR RIBONUCLEOPROTEIN F
	Chains	:	F, I
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	SNRPF
	Organism Common	:	CLAWED FROG,COMMON PLATANNA,PLATANNA
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355
	Synonym	:	SNRNP-F, SM PROTEIN F, SM-F, SMF

Molecule 5 - SMALL NUCLEAR RIBONUCLEOPROTEIN G
	Chains	:	G, J
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	SNRPG
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	SNRNP-G, SM PROTEIN G, SM-G, SMG

Molecule 6 - ICLN PROTEIN
	Chains	:	Q, P
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	CG4924, ICLN
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	SD10511P

		1	2	3	4	5	6	7	8	9	10	11	12
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J	P	Q
Biological Unit 1 (1x)	:	A	B			E	F	G				P
Biological Unit 2 (1x)	:			C	D				H	I	J		Q

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	P6G	-1	Ligand/Ion	HEXAETHYLENE GLYCOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR F:4015 , GLY F:4016 , LYS F:4017 , PHE H:3050 , ASP H:3051 , GLU H:3052 , ASN I:4006	BINDING SITE FOR RESIDUE P6G H 3101

(no "SS Bond" information available for 4F7U)

Asymmetric Unit

No.	Residues
1	Asn D:2112	-	Pro D:2113
2	Leu I:4003	-	Pro I:4004
3	Asn P:6068	-	Pro P:6069

(no "SAP(SNP)/Variant" information available for 4F7U)

(no "PROSITE Motif" information available for 4F7U)

(no "Exon" information available for 4F7U)

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:82
                                                                                                                   
               SCOP domains d4f7ua_ A: D1 core SNRNP protein                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.....eeeeee....eeeeeeeee.....eeeeeeeee......eeeeeeee....eeeee.....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                4f7u A 1001 MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLVD 1082
                                  1010      1020      1030      1040      1050      1060      1070      1080

Chain B from PDB  Type:PROTEIN  Length:80
                                                                                                                 
               SCOP domains d4f7ub_ B: D2 core SNRNP protein                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.hhhhhhhhhh..eeeeee....eeeeeeeee.....eeeeeeeeee....eeeeeeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                4f7u B 2022 EEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVNKDRYISKMFLRGDSVIVVLRNPL 2114
                                  2031      2041      2051      2061      2071    ||2094      2104      2114
                                                                               2076|                        
                                                                                2090

Chain C from PDB  Type:PROTEIN  Length:81
                                                                                                                  
               SCOP domains d4f7uc_ C: D1 core SNRNP protein                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.....eeeeee....eeeeeeeee.....eeeeeeeee......eeeeeeee....eeeee.....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                4f7u C 1002 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLVD 1082
                                  1011      1021      1031      1041      1051      1061      1071      1081

Chain D from PDB  Type:PROTEIN  Length:85
                                                                                                                      
               SCOP domains d4f7ud_ D: D2 core SNRNP protein                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.hhhhhhhhhhh..eeeee...eeeeeeeeee.....eeeeeeeeee....eeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                4f7u D 2016 LQKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVNKDRYISKMFLRGDSVIVVLRNP 2113
                                  2025      2035      2045      2055      2065      2075||    2098      2108     
                                                                                     2076|                       
                                                                                      2090

Chain E from PDB  Type:PROTEIN  Length:78
                                                                                                               
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.eeeeee.....eeeeeeeeee.....eeeeeeeeee....eeeeeeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                4f7u E 3013 VMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQSV 3090
                                  3022      3032      3042      3052      3062      3072      3082

Chain F from PDB  Type:PROTEIN  Length:73
                                                                                                          
               SCOP domains d4f7uf_ F: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..eeeeee....eeeeeeeee.....eeeeeeeeee..eeeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                4f7u F 4004 PLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVE 4076
                                  4013      4023      4033      4043      4053      4063      4073

Chain G from PDB  Type:PROTEIN  Length:68
                                                                                                     
               SCOP domains d4f7ug_ G: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..eeeeee...eeeeeeeeee.....eeeeeeeee.....eeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                4f7u G 5007 PELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIMLEALE 5074
                                  5016      5026      5036      5046      5056      5066

Chain H from PDB  Type:PROTEIN  Length:78
                                                                                                               
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.eeeeee.....eeeeeeeeee.....eeeeeeeeee....eeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                4f7u H 3014 MVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQSVS 3091
                                  3023      3033      3043      3053      3063      3073      3083

Chain I from PDB  Type:PROTEIN  Length:74
                                                                                                           
               SCOP domains d4f7ui_ I: automated matches                                               SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh...eeeeee....eeeeeeeee.....eeeeeeeeee..eeeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                4f7u I 4003 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVE 4076
                                  4012      4022      4032      4042      4052      4062      4072

Chain J from PDB  Type:PROTEIN  Length:67
                                                                                                    
               SCOP domains d4f7uj_ J: automated matches                                        SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeeeee...eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                4f7u J 5008 ELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIMLEALE 5074
                                  5017      5027      5037      5047      5057      5067

Chain P from PDB  Type:PROTEIN  Length:116
                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee........eeeeeeeeeeee..eeeeeeeeeee..eeeeee.....eeeee...eeeeeeee...eeeeeee............eeeeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                4f7u P 6001 MVLIMHVSPPEHGLLYTANNIKLKLGDKVVGEGTVYIAQNTLSWQPTELAEGISIEWKQVSLHGISSNPRKCIYFMLDHKVEWNGVYEVTECWLMPEDIATVDTMYSAMTTCQALH 6160
                                  6010      6020      6030      6040      6050      6060      6070      6080      6134      6144      6154      
                                                                                                               6087|                            
                                                                                                                6132

Chain Q from PDB  Type:PROTEIN  Length:120
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee........eeeeeeeeeeee...eeeeeeeeee..eeeeee.....eeeee...eeeeeeee...eeeeeee..............eeeeeee...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                4f7u Q 6001 MVLIMHVSPPEHGLLYTANNIKLKLGDKVVGEGTVYIAQNTLSWQPTELAEGISIEWKQVSLHGISSNPRKCIYFMLDHKVEWNGVYGGEVTECWLMPEDIATVDTMYSAMTTCQALHHH 6162
                                  6010      6020      6030      6040      6050      6060      6070      6080      6132      6142      6152      6162
                                                                                                                6088|                               
                                                                                                                 6131

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 4F7U)

(no "Pfam Domain" information available for 4F7U)

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	Cis Peptide Bonds
		Asn D:2112 - Pro D:2113	[ RasMol ]
		Asn P:6068 - Pro P:6069	[ RasMol ]
		Leu I:4003 - Pro I:4004	[ RasMol ]

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	RUXF_HUMAN \| P62306	:	3cw1 3jcr 3pgw 3s6n 4pjo 4v98 4wzj 5mqf
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(no "Related Entries Specified in the PDB File" available for 4F7U)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (4, 8)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (46, 270)

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Related Entries Specified in the PDB File