4CG5 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYO-EM OF THE SEC61-COMPLEX BOUND TO THE 80S RIBOSOME TRANSLATING A SECRETORY SUBSTRATE

Authors :   M. Gogala, T. Becker, B. Beatrix, C. Barrio-Garcia, O. Berninghausen, R. Beckmann

Date :   21 Nov 13 (Deposition) - 05 Feb 14 (Release) - 19 Feb 14 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   7.40

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Protein Transport, Ribosome, Co-Translational Protein Translocation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Gogala, T. Becker, B. Beatrix, J. Armache, C. Barrio-Garcia, O. Berninghausen, R. Beckmann
Structures Of The Sec61 Complex Engaged In Nascent Peptide Translocation Or Membrane Insertion.
Nature V. 506 107 2014
PubMed-ID: 24499919 | Reference-DOI: 10.1038/NATURE12950

Molecule 1 - PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1
	Chains	:	A
	Organ	:	PANCREAS
	Organism Common	:	DOG
	Organism Scientific	:	CANIS LUPUS FAMILIARIS
	Organism Taxid	:	9615
	Synonym	:	SEC61 ALPHA-1

Molecule 2 - PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA
	Chains	:	C
	Fragment	:	RESIDUES 61-96
	Organ	:	PANCREAS
	Organism Common	:	DOG
	Organism Scientific	:	CANIS LUPUS FAMILIARIS
	Organism Taxid	:	9615
	Synonym	:	TRANSPORT PROTEIN SEC61 SUBUNIT BETA

Molecule 3 - PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA
	Chains	:	B
	Organ	:	PANCREAS
	Organism Common	:	DOG
	Organism Scientific	:	CANIS LUPUS FAMILIARIS
	Organism Taxid	:	9615

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4CG5)

(no "Site" information available for 4CG5)

(no "SS Bond" information available for 4CG5)

(no "Cis Peptide Bond" information available for 4CG5)

(no "SAP(SNP)/Variant" information available for 4CG5)

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SECE_SEC61G	PS01067	Protein secE/sec61-gamma signature.	SC61G_CANLF	14-42	1	B:14-42
2	SECY_1	PS00755	Protein secY signature 1.	S61A1_CANLF	75-94	1	A:75-94
3	SECY_2	PS00756	Protein secY signature 2.	S61A1_CANLF	164-182	1	A:164-182

(no "Exon" information available for 4CG5)

Asymmetric/Biological 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:452
 aligned with S61A1_CANLF | P38377 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:452
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474  
          S61A1_CANLF    25 KIQFKEKVLWTAITLFIFLVCCQIPLFGIMSSDSADPFYWMRVILASNRGTLMELGISPIVTSGLIMQLLAGAKIIEVGDTPKDRALFNGAQKLFGMIITIGQSIVYVMTGMYGDPSEMGAGICLLITIQLFVAGLIVLLLDELLQKGYGLGSGISLFIATNICETIVWKAFSPTTVNTGRGMEFEGAIIALFHLLATRTDKVRALREAFYRQNLPNLMNLIATIFVFAVVIYFQGFRVDLPIKSARYRGQYNTYPIKLFYTSNIPIILQSALVSNLYVISQMLSARFSGNLLVSLLGTWSDTSSGGPARAYPVGGLCHYLSPPESFGSVLEDPVHAVVYIVFMLGSCAFFSKTWIEVSGSSAKDVAKQLKEQQMVMRGHRETSMVHELNRYIPTAAAFGGLCIGALSVLADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEVGSMGALLF 476
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh...........hhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh................hhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------SECY_1  PDB: A:75-94---------------------------------------------------------------------SECY_2             ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cg5 A  25 KIQFKEKVLWTAITLFIFLVCCQIPLFGIMSSDSADPFYWMRVILASNRGTLMELGISPIVTSGLIMQLLAGAKIIEVGDTPKDRALFNGAQKLFGMIITIGQSIVYVMTGMYGDPSEMGAGICLLITIQLFVAGLIVLLLDELLQKGYGLGSGISLFIATNICETIVWKAFSPTTVNTGRGMEFEGAIIALFHLLATRTDKVRALREAFYRQNLPNLMNLIATIFVFAVVIYFQGFRVDLPIKSARYRGQYNTYPIKLFYTSNIPIILQSALVSNLYVISQMLSARFSGNLLVSLLGTWSDTSSGGPARAYPVGGLCHYLSPPESFGSVLEDPVHAVVYIVFMLGSCAFFSKTWIEVSGSSAKDVAKQLKEQQMVMRGHRETSMVHELNRYIPTAAAFGGLCIGALSVLADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEVGSMGALLF 476
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474

Chain B from PDB  Type:PROTEIN  Length:62
 aligned with SC61G_CANLF | P60058 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:62
                                    16        26        36        46        56        66  
          SC61G_CANLF     7 FVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIPINNIIVGG  68
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------SECE_SEC61G  PDB: B:14-42    -------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 4cg5 B   7 FVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIPINNIIVGG  68
                                    16        26        36        46        56        66

Chain C from PDB  Type:PROTEIN  Length:36
 aligned with SC61B_CANLF | P60467 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:36
                                    70        80        90      
          SC61B_CANLF    61 EDSPGLKVGPVPVLVMSLLFIASVFMLHIWGKYTRS  96
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                 4cg5 C  61 EDSPGLKVGPVPVLVMSLLFIASVFMLHIWGKYTRS  96
                                    70        80        90

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 4CG5)

(no "CATH Domain" information available for 4CG5)

(no "Pfam Domain" information available for 4CG5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (S61A1_CANLF | P38377)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0045047	protein targeting to ER	The process of directing proteins towards the endoplasmic reticulum (ER) using signals contained within the protein. One common mechanism uses a 16- to 30-residue signal sequence, typically located at the N-terminus of the protein and containing positively charged amino acids followed by a continuous stretch of hydrophobic residues, which directs the ribosome to the ER membrane and initiates transport of the growing polypeptide across the ER membrane.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0030176	integral component of endoplasmic reticulum membrane	The component of the endoplasmic reticulum membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B (SC61G_CANLF | P60058)

molecular function
	GO:0015450	P-P-bond-hydrolysis-driven protein transmembrane transporter activity	Primary active carrier-mediated transport of a protein across a membrane, driven by the hydrolysis of the diphosphate bond of inorganic pyrophosphate, ATP, or another nucleoside triphosphate. The transport protein may or may not be transiently phosphorylated, but the substrate is not phosphorylated.
	GO:0008565	protein transporter activity	Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
	GO:0006886	intracellular protein transport	The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
	GO:0006605	protein targeting	The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
	GO:0045047	protein targeting to ER	The process of directing proteins towards the endoplasmic reticulum (ER) using signals contained within the protein. One common mechanism uses a 16- to 30-residue signal sequence, typically located at the N-terminus of the protein and containing positively charged amino acids followed by a continuous stretch of hydrophobic residues, which directs the ribosome to the ER membrane and initiates transport of the growing polypeptide across the ER membrane.
	GO:0071806	protein transmembrane transport	The directed movement of a protein across a membrane by means of some agent such as a transporter or pore.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0030176	integral component of endoplasmic reticulum membrane	The component of the endoplasmic reticulum membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain C (SC61B_CANLF | P60467)

molecular function
	GO:0015450	P-P-bond-hydrolysis-driven protein transmembrane transporter activity	Primary active carrier-mediated transport of a protein across a membrane, driven by the hydrolysis of the diphosphate bond of inorganic pyrophosphate, ATP, or another nucleoside triphosphate. The transport protein may or may not be transiently phosphorylated, but the substrate is not phosphorylated.
	GO:0048408	epidermal growth factor binding	Interacting selectively and non-covalently with epidermal growth factor.
biological process
	GO:0006886	intracellular protein transport	The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
	GO:0000060	protein import into nucleus, translocation	A protein transport process that contributes to protein import into the nucleus, and that results in the vectorial transfer of a cargo-carrier protein complex through the nuclear pore complex from the cytoplasmic side to the nucleoplasmic side of the nuclear envelope.
	GO:0071806	protein transmembrane transport	The directed movement of a protein across a membrane by means of some agent such as a transporter or pore.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0030970	retrograde protein transport, ER to cytosol	The directed movement of unfolded or misfolded proteins from the endoplasmic reticulum to the cytosol through the translocon.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
	GO:0030433	ubiquitin-dependent ERAD pathway	The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
cellular component
	GO:0005784	Sec61 translocon complex	A translocon complex that contains a core heterotrimer of conserved alpha, beta and gamma subunits, and may contain additional proteins (translocon-associated proteins or TRAPs); in budding yeast the core proteins are Sec61p, Sbh1p, and Sss1p. The Sec61 translocon complex functions in cotranslational and posttranslational translocation events.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0031205	endoplasmic reticulum Sec complex	An endoplasmic reticulum membrane-associated complex involved in the translocation of proteins that are targeted to the ER. In yeast, this complex consists of two subcomplexes, namely, the Sec61 complex and the Sec62/Sec63 complex.
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	S61A1_CANLF \| P38377
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	SC61B_CANLF \| P60467
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	SC61G_CANLF \| P60058
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	SC61G_CANLF \| P60058
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UniProtKB/Swiss-Prot
	S61A1_CANLF \| P38377	:	2wwb 3jc2 4cg6 4cg7 5a6u
	SC61B_CANLF \| P60467	:	2wwb 4cg6 4cg7 5a6u
	SC61G_CANLF \| P60058	:	2wwb 3jc2 4cg6 4cg7 5a6u

4cg6	CRYO-EM OF THE SEC61-COMPLEX BOUND TO THE IDLE 80S RIBOSOME
4cg7	CRYO-EM OF THE SEC61-COMPLEX BOUND TO THE IDLE 80S RIBOSOME

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