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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYO-EM RECONSTRUCTION OF THE METAVINCULIN-ACTIN INTERFACE

Authors :   L. Y. Kim, P. M. Thompson, H. T. Lee, M. Pershad, S. L. Campbell, G. M. Alus

Date :   03 Sep 15 (Deposition) - 04 Nov 15 (Release) - 17 Feb 16 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   8.20

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

Keywords :   Actin, Metavinculin, Vinculin, Cell Migration, Adhesion, Mechanosensation, Cytoskeleton, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Y. Kim, P. M. Thompson, H. T. Lee, M. Pershad, S. L. Campbell, G. M. Alushin
The Structural Basis Of Actin Organization By Vinculin And Metavinculin.
J. Mol. Biol. V. 428 10 2016
PubMed-ID: 26493222 | Reference-DOI: 10.1016/J.JMB.2015.09.031

Molecule 1 - ACTIN, ALPHA SKELETAL MUSCLE
	Chains	:	A, B
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	Synonym	:	ALPHA-ACTIN-1
	Tissue	:	SKELETAL MUSCLE

Molecule 2 - METAVINCULIN
	Chains	:	M
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	2HR-T
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	TAIL DOMAIN (UNP RESIDUES 858-1129)
	Gene	:	VCL
	Organelle	:	FOCAL ADHESION
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MVT

		1	2	3
Asymmetric/Biological Unit	:	A	B	M

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:137 , ASP A:154 , ADP A:402	BINDING SITE FOR RESIDUE MG A 401
2	AC2	SOFTWARE	GLY A:13 , SER A:14 , LEU A:16 , LYS A:18 , GLN A:137 , ASP A:154 , GLY A:156 , ASP A:157 , ARG A:210 , GLU A:214 , GLY A:301 , GLY A:302 , THR A:303 , MET A:305 , TYR A:306 , MG A:401	BINDING SITE FOR RESIDUE ADP A 402
3	AC3	SOFTWARE	GLN B:137 , ASP B:154 , ADP B:402	BINDING SITE FOR RESIDUE MG B 401
4	AC4	SOFTWARE	GLY B:13 , SER B:14 , LEU B:16 , LYS B:18 , GLN B:137 , ASP B:154 , GLY B:156 , ASP B:157 , ARG B:210 , LYS B:213 , GLU B:214 , GLY B:301 , GLY B:302 , THR B:303 , MET B:305 , TYR B:306 , MG B:401	BINDING SITE FOR RESIDUE ADP B 402

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:15	-	Leu A:16
2	Gly A:23	-	Asp A:24
3	Gly A:46	-	Met A:47
4	Gly A:55	-	Asp A:56
5	Lys A:113	-	Ala A:114
6	Asp A:157	-	Gly A:158
7	Glu A:167	-	Gly A:168
8	Ala A:181	-	Gly A:182
9	Ile A:309	-	Ala A:310
10	Ser A:350	-	Thr A:351
11	Gly B:15	-	Leu B:16
12	Gly B:23	-	Asp B:24
13	Gly B:46	-	Met B:47
14	Gly B:55	-	Asp B:56
15	Lys B:113	-	Ala B:114
16	Asp B:157	-	Gly B:158
17	Glu B:167	-	Gly B:168
18	Ala B:181	-	Gly B:182
19	Ile B:309	-	Ala B:310
20	Ser B:350	-	Thr B:351

(no "SAP(SNP)/Variant" information available for 3JBK)

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

(no "Exon" information available for 3JBK)

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:367
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeeee.......eee...eeee.................hhhhhh...eeee..ee..ee.hhhhhhhhhhhhhhhh.........eeeee......hhhhhhhhhhhhhhh..eeeeeehhhhhhhhh....eeeeeee..eeeeeeee..ee.hhhheee...hhhhhhhhhhhhhh.........hhhhhhhhhhhh.....hhhhhhhhhhh.....eeee.....eeeehhhhhhhhhh............hhhhhhhhhhh..hhhhhhhhh..eee.hhhhh....hhhhhhhhhhhh.......ee...hhhhhhhhhhhhhhhh.hhhhhheehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3jbk A    5 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVH  371
                                    14        24        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

Chain B from PDB  Type:PROTEIN  Length:367
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeeee.......eee...eeee..............ee.hhhhhh...eeee..ee..ee.hhhhhhhhhhhhhhhh.........eeeee......hhhhhhhhhhhhhh...ee.eeehhhhhhhhhh...eeeeeee..eeeeeeee..ee.hhhheee...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.....hhhhhhhhhhh.....eeee.....eeeehhhhhhhhhh............hhhhhhhhhhh..hhhhhhhhh...ee.hhhhh....hhhhhhhhhhhh............hhhhhhhhhhhhhhhh.hhhhhheehhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3jbk B    5 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVH  371
                                    14        24        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

Chain M from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                3jbk M  917 NDIIAAAKRMALLMAEMSRLVRGGSGTKRALIQCAKDIAKASDEVTRLAKEVAKQCTDKRIRTNLLQVCERIPTISTQLKILSTVKATMLGRTNISDEESEQATEMLVHNAQNLMQSVKETVREAEAASIK 1047
                                   926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046

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 3JBK)

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

(no "Pfam Domain" information available for 3JBK)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		ADP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:181 - Gly A:182	[ RasMol ]
		Ala B:181 - Gly B:182	[ RasMol ]
		Asp A:157 - Gly A:158	[ RasMol ]
		Asp B:157 - Gly B:158	[ RasMol ]
		Glu A:167 - Gly A:168	[ RasMol ]
		Glu B:167 - Gly B:168	[ RasMol ]
		Gly A:15 - Leu A:16	[ RasMol ]
		Gly A:23 - Asp A:24	[ RasMol ]
		Gly A:46 - Met A:47	[ RasMol ]
		Gly A:55 - Asp A:56	[ RasMol ]
		Gly B:15 - Leu B:16	[ RasMol ]
		Gly B:23 - Asp B:24	[ RasMol ]
		Gly B:46 - Met B:47	[ RasMol ]
		Gly B:55 - Asp B:56	[ RasMol ]
		Ile A:309 - Ala A:310	[ RasMol ]
		Ile B:309 - Ala B:310	[ RasMol ]
		Lys A:113 - Ala A:114	[ RasMol ]
		Lys B:113 - Ala B:114	[ RasMol ]
		Ser A:350 - Thr A:351	[ RasMol ]
		Ser B:350 - Thr B:351	[ RasMol ]

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		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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	VINC_HUMAN \| P18206
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (20, 20)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (62, 65)

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