4WNL - JenaLib

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Title :   THE X-RAY STRUCTURE OF A RNA-BINDING PROTEIN COMPLEX

Authors :   N. Singh, G. Blobel, H. Shi

Date :   13 Oct 14 (Deposition) - 24 Dec 14 (Release) - 14 Jan 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Rna-Binding, Mrna Transport, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Singh, G. Blobel, H. Shi
Hooking She3P Onto She2P For Myosin-Mediated Cytoplasmic Mrna Transport.
Proc. Natl. Acad. Sci. Usa V. 112 142 2015
PubMed-ID: 25535369 | Reference-DOI: 10.1073/PNAS.1423194112

Molecule 1 - SWI5-DEPENDENT HO EXPRESSION PROTEIN 2
	Chains	:	C, A, B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	SHE2, YKL130C
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C

Molecule 2 - SWI5-DEPENDENT HO EXPRESSION PROTEIN 3
	Chains	:	E, F, G, H
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 342-374
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	545124
	Synthetic	:	YES

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A		C			F	G
Biological Unit 2 (1x)	:		B		D	E			H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	IPA	2	Ligand/Ion	ISOPROPYL ALCOHOL
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 7)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER B:127 , ALA C:46 , THR C:47 , PHE C:50	binding site for residue GOL C 301
02	AC2	SOFTWARE	GLU C:160 , SER C:166 , ASN C:167 , ASP C:170	binding site for residue GOL C 302
03	AC3	SOFTWARE	LEU A:97 , ILE A:164 , SER A:166 , LEU A:169 , PRO D:98	binding site for residue SO4 A 301
04	AC4	SOFTWARE	ASN A:149 , ASN A:193 , ILE A:194	binding site for residue SO4 A 302
05	AC5	SOFTWARE	ASN A:131	binding site for residue IPA A 303
06	AC6	SOFTWARE	ASN B:193 , ILE B:194	binding site for residue SO4 B 301
07	AC7	SOFTWARE	PRO B:87	binding site for residue SO4 B 302
08	AC8	SOFTWARE	ALA B:46 , THR B:47 , ARG B:49 , LYS B:128 , GLU C:124 , SER C:127	binding site for residue GOL B 303
09	AC9	SOFTWARE	LYS B:57 , LYS B:60 , TYR C:115	binding site for residue GOL B 304
10	AD1	SOFTWARE	GLU B:160 , SER B:166 , ASP B:170 , GLN B:175	binding site for residue GOL B 305
11	AD2	SOFTWARE	ALA D:46 , ARG D:49 , PHE D:50	binding site for residue IPA D 301
12	AD3	SOFTWARE	ASN B:131 , GLU B:132 , ASP B:133 , LEU D:130 , ASN D:131 , GLU D:132 , ASP D:133	binding site for residue GOL D 302

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

Asymmetric Unit

No.	Residues
1	Pro C:87	-	Gly C:88
2	Thr C:186	-	Asn C:187
3	Glu C:190	-	Thr C:191
4	Pro E:362	-	Val E:363
5	Val E:363	-	Leu E:364

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

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

(no "Exon" information available for 4WNL)

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:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wnl A   6 DIKVTPGTSELVEQILALLSRYLSSYIHVLNKFISHLRRVATLRFERTTLIKFVKKLRFYNDSVLSYNASEFINEPGADSFDKVILPIASMFVKCVETFDLLNYYLTQSLQKEILSKTLNEDLTLTAESILAIDDTYNHFVKFSQWMIESLRIGSNLLDLEVVQFAIKSADEDGTNIGETDNIFLQEILPVNSEEEFQTLSAAWHSILDGKLGALDEEFDVVATKWH 238
                                    15        25        35        45        55        65        75    ||  91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
                                                                                                     80|                                                                                                                                                       
                                                                                                      87

Chain B from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wnl B   6 DIKVTPGTSELVEQILALLSRYLSSYIHVLNKFISHLRRVATLRFERTTLIKFVKKLRFYNDSVLSYNASEFINEPGADSFDKVILPIASMFVKCVETFDLLNYYLTQSLQKEILSKTLNEDLTLTAESILAIDDTYNHFVKFSQWMIESLRIGSNLLDLEVVQFAIKSADEDGTDNIFLQEILPVNSEEEFQTLSAAWHSILDGKLGALDEEFDVVATKWH 238
                                    15        25        35        45        55        65        75    ||  91       101       111       121       131       141       151       161       171       181   ||  196       206       216       226       236  
                                                                                                     80|                                                                                               185|                                               
                                                                                                      87                                                                                                191

Chain C from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.......hhhhhee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wnl C   6 DIKVTPGTSELVEQILALLSRYLSSYIHVLNKFISHLRRVATLRFERTTLIKFVKKLRFYNDSVLSYNASEFINEGKNPGADSFDKVILPIASMFVKCVETFDLLNYYLTQSLQKEILSKTLNEDLTLTAESILAIDDTYNHFVKFSQWMIESLRIGSNLLDLEVVQFAIKSADEDGTNIGETDNIFLQEILPVNSEEEFQTLSAAWHSILDGKLGALDEEFDVVATKWHD 239
                                    15        25        35        45        55        65        75       |88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238 
                                                                                                        83|                                                                                                                                                        
                                                                                                         87

Chain D from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wnl D   6 DIKVTPGTSELVEQILALLSRYLSSYIHVLNKFISHLRRVATLRFERTTLIKFVKKLRFYNDSVLSYNASEFINEADSFDKVILPIASMFVKCVETFDLLNYYLTQSLQKEILSKTLNEDLTLTAESILAIDDTYNHFVKFSQWMIESLRIGSNLLDLEVVQFAIKSADEDGTDNIFLQEILPVNSEEEFQTLSAAWHSILDGKLGALDEEFDVVATKWH 238
                                    15        25        35        45        55        65        75    ||  93       103       113       123       133       143       153       163       173       183 ||    198       208       218       228       238
                                                                                                     80|                                                                                             185|                                               
                                                                                                      89                                                                                              191

Chain E from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4wnl E 362 PVLPGVKR 369

Chain F from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author .....ee. Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4wnl F 362 PVLPGVKR 369

Chain G from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4wnl G 362 PVLPGVKR 369

Chain H from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4wnl H 363 VLPGVK 368

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 4WNL)

(no "CATH Domain" information available for 4WNL)

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

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Asymmetric Unit
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	Cis Peptide Bonds
		Glu C:190 - Thr C:191	[ RasMol ]
		Pro C:87 - Gly C:88	[ RasMol ]
		Pro E:362 - Val E:363	[ RasMol ]
		Thr C:186 - Asn C:187	[ RasMol ]
		Val E:363 - Leu E:364	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (15, 31)

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Related Entries Specified in the PDB File