3J7I - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF ALPHA- AND BETA- TUBULIN IN GMPCPP-MICROTUBULES

Authors :   H. Yajima, T. Ogura, R. Nitta, Y. Okada, C. Sato, N. Hirokawa

Date :   01 Jul 14 (Deposition) - 10 Dec 14 (Release) - 10 Dec 14 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   8.90

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

Keywords :   Microtubule, Tubulin, Gtp-State Structure, Gmpcpp, Microtubule Stabilaization, Micotubule Polymerization, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Yajima, T. Ogura, R. Nitta, Y. Okada, C. Sato, N. Hirokawa
Conformational Changes In Tubulin In Gmpcpp And Gdp-Taxol Microtubules Observed By Cryoelectron Microscopy
J. Cell Biol. V. 198 315 2012
PubMed-ID: 22851320 | Reference-DOI: 10.1083/JCB.201201161
(for further references see the PDB file header)

Molecule 1 - TUBULIN ALPHA-1A CHAIN
	Chains	:	A
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823
	Synonym	:	ALPHA-TUBULIN 1, TUBULIN ALPHA-1 CHAIN
	Tissue	:	BRAIN

Molecule 2 - TUBULIN BETA CHAIN
	Chains	:	B
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823
	Synonym	:	BETA-TUBULIN
	Tissue	:	BRAIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	GTP	2	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:69 , GLU A:71 , VAL A:74 , GTP A:502	BINDING SITE FOR RESIDUE MG A 501
2	AC2	SOFTWARE	GLY A:10 , GLN A:11 , ALA A:12 , GLN A:15 , ILE A:16 , ASP A:69 , LEU A:70 , GLU A:71 , ILE A:171 , TYR A:224 , ASN A:228 , MG A:501 , PRO B:245 , GLY B:246 , GLN B:247	BINDING SITE FOR RESIDUE GTP A 502
3	AC3	SOFTWARE	GLU B:71 , GTP B:502	BINDING SITE FOR RESIDUE MG B 501
4	AC4	SOFTWARE	GLN B:11 , CYS B:12 , GLN B:15 , ASN B:206 , TYR B:224 , LEU B:227 , ASN B:228 , MG B:501	BINDING SITE FOR RESIDUE GTP B 502

(no "SS Bond" information available for 3J7I)

Asymmetric/Biological Unit

No.	Residues
1	Pro A:173	-	Ala A:174

Asymmetric/Biological Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TBB_PIG_001 *	H	37	V	TBB_PIG	---	---	B	H	37	V
2	UniProt	VAR_TBB_PIG_002 *	N	48	S	TBB_PIG	---	---	B	N	50	S
3	UniProt	VAR_TBA1A_PIG_001 *	A	265	G	TBA1A_PIG	---	---	A	G	265	G
4	UniProt	VAR_TBA1A_PIG_002 *	A	265	I	TBA1A_PIG	---	---	A	G	265	I
5	UniProt	VAR_TBA1A_PIG_003 *	H	266	I	TBA1A_PIG	---	---	A	H	266	I
6	UniProt	VAR_TBB_PIG_003 *	S	275	A	TBB_PIG	---	---	B	S	277	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TUBULIN	PS00227	Tubulin subunits alpha, beta, and gamma signature.	TBB_PIG	140-146	1	B:142-148
1	TUBULIN	PS00227	Tubulin subunits alpha, beta, and gamma signature.	TBA1A_PIG	142-148	1	A:142-148

(no "Exon" information available for 3J7I)

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:409
 aligned with TBA1A_PIG | P02550 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:437
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       
            TBA1A_PIG     2 RECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRAHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVD 438
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhhhhhhhhhhhhh.......--------------------------....eeee..hhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhh-...eeeeee.......hhhhhhhhhhhhhh.-....eeeee...........hhhhhhhhhhh......eeeee..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh........eee...............hhhhhhhhhh...............eeeeeeeeee..hhhhhhhhhhhhhh.............eeeee.................eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GI---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------TUBULIN-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j7i A   2 RECISIHVGQAGVQIGNACWELYCLEHGIQPDG--------------------------HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQC-GLQGFSVFHSFGGGTGSGFTSLLMERLSVDY-KKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVD 438
                                    11        21        31  |      -         -        61        71        81        91       101       111       121       131       141       151       161 |     171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       
                                                           34                         61                                                                 129 |                           161 |                                                                                                                                                                                                                                                                                   
                                                                                                                                                           131                             163

Chain B from PDB  Type:PROTEIN  Length:411
 aligned with TBB_PIG | P02554 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:425
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421     
              TBB_PIG     2 REIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQ 426
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.hhhhhhhhhhhhhhhhh..................hhhhhh...........eeee..hhhhhhhhh..hhhhh.hhh.ee.--.............hhhhhhhhhhhhhhhhhh.--...eeeeee--.hhhhhhhhhhhhhhhh..---.eeeeee...-----....hhhhhhhhhhhhhhh.......hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh........eee................hhhhhhhhh.........hhhhh....eeeeee...hhhhhhhhhhhhhhhh...........eeeeee..........eeeee.......hhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------V----------S----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------TUBULIN---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j7i B   2 REIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVF--SGAGNNWAKGHYTEGAELVDSVLDVVRKESES--CLQGFQLTH--GGGTGSGMGTLLISKIREE---RIMNTFSVVP-----DTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQ 436
                                    11        21        31        41  ||    53        63        73        83        93|  |   103       113       123    |  133     | 143       153      |  -|      173     | 183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353      |371       381|||    391       401       411       421       431     
                                                                     44|                                             94 97                            128  |     139  |               160 164      173   179                                                                                                                                                                                  360|          382||                                                    
                                                                      47                                                                                 131        142                                                                                                                                                                                                                        369           363|                                                    
                                                                                                                                                                                                                                                                                                                                                                                                              384

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 3J7I)

(no "CATH Domain" information available for 3J7I)

(no "Pfam Domain" information available for 3J7I)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TBA1A_PIG | P02550)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005200	structural constituent of cytoskeleton	The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
biological process
	GO:0007017	microtubule-based process	Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005874	microtubule	Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.

Chain B (TBB_PIG | P02554)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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).
	GO:0005200	structural constituent of cytoskeleton	The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
biological process
	GO:0007017	microtubule-based process	Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005874	microtubule	Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Pro A:173 - Ala A:174	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3J7I)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (6, 6)

PROSITE Motifs (1, 2)

Exons (0, 0)

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