1TUB - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   TUBULIN ALPHA-BETA DIMER, ELECTRON DIFFRACTION

Authors :   E. Nogales, K. H. Downing

Date :   23 Sep 97 (Deposition) - 07 Oct 98 (Release) - 24 Feb 09 (Revision)

Method :   ELECTRON CRYSTALLOGRAPHY

Resolution :   3.70

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

Keywords :   Microtubules, Alpha-Tubulin, Beta-Tubulin, Gtpase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Nogales, S. G. Wolf, K. H. Downing
Structure Of The Alpha Beta Tubulin Dimer By Electron Crystallography.
Nature V. 391 199 1998
PubMed-ID: 9428769 | Reference-DOI: 10.1038/34465
(for further references see the PDB file header)

Molecule 1 - TUBULIN
	Chains	:	A
	Organ	:	BRAIN
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823

Molecule 2 - TUBULIN
	Chains	:	B
	Organ	:	BRAIN
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
3	TXL	1	Ligand/Ion	TAXOTERE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN B:11 , CYS B:12 , GLN B:15 , ASN B:101 , SER B:140 , GLY B:143 , GLY B:144 , THR B:145 , SER B:178 , TYR B:185 , ASN B:206	BINDING SITE FOR RESIDUE GDP B 500
2	AC2	SOFTWARE	GLN A:11 , ALA A:12 , GLU A:71 , ALA A:100 , ASN A:101 , GLY A:143 , GLY A:144 , THR A:145 , ASN A:206 , TYR A:224 , LEU A:227 , ASN A:228 , LEU B:248 , LYS B:254	BINDING SITE FOR RESIDUE GTP A 500
3	AC3	SOFTWARE	VAL B:23 , LEU B:217 , ASP B:226 , HIS B:229 , SER B:236 , PHE B:272 , PRO B:274 , LEU B:275 , THR B:276 , ARG B:278 , ARG B:320 , ARG B:369 , GLY B:370 , LEU B:371	BINDING SITE FOR RESIDUE TXL B 501

(no "SS Bond" information available for 1TUB)

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:357	-	Glu A:358
2	Leu B:194	-	Val B:195

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 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TUBULIN_B_AUTOREG	PS00228	Tubulin-beta mRNA autoregulation signal.	TBB_PIG	1-4	1	B:1-4
2	TUBULIN	PS00227	Tubulin subunits alpha, beta, and gamma signature.	TBB_PIG	140-146	1	B:142-148
2	TUBULIN	PS00227	Tubulin subunits alpha, beta, and gamma signature.	TBA1A_PIG	142-148	1	A:142-148

(no "Exon" information available for 1TUB)

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:440
 aligned with TBA1A_PIG | P02550 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:440
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440
            TBA1A_PIG     1 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRAHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSV 440
               SCOP domains d1tuba1 A:1-245 Tubulin alpha-subunit                                                                                                                                                                                                                d1tuba2 A:246-440 Tubulin alpha-subunit                                                                                                                                                             SCOP domains
               CATH domains 1tubA01 A:1-268  [code=3.40.50.1440, no name defined]                                                                                                                                                                                                                       1tubA02 A:269-383  [code=3.30.1330.20, no name defined]                                                            1tubA03 A:384-440 Helix hairpin bin                       CATH domains
               Pfam domains --Tubulin-1tubA01 A:3-226                                                                                                                                                                                                         ------------------------------------Tubulin_C-1tubA02 A:263-393                                                                                                        ----------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhh.........................................eeeeee...hhhhhh.............eeee..............hhhhhhhhhhhhhhhhh......eeeeeee.....hhhhhhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhh......eeeee.hhhhhhhhhh.........hhhhhhhhhhhhhhh............hhhhhhhh......eeeeeeee..............hhhhhhhh..................eeeeeee....hhhhhhhhhhhhh.............eeeeee................eeeeeeee....hhhhhhhhhhhhh....................hhhhhhhhhhhhhhhh....... Sec.struct. author
             SAPs(SNPs) (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------TUBULIN---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tub A   1 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSV 440
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440

Chain B from PDB  Type:PROTEIN  Length:427
 aligned with TBB_PIG | P02554 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:427
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       
              TBB_PIG     1 MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQD 427
               SCOP domains d1tubb1 B:1-245 Tubulin beta-subunit                                                                                                                                                                                                               d1tubb2 B:246-437 Tubulin beta-subunit                                                                                                                                                   SCOP domains
               CATH domains 1tubB01 B:1-261  [code=3.40.50.1440, no name defined]                                                                                                                                                                                                              1tubB02 B:262-383  [code=3.30.1330.20, no name defined]                                                           1tubB03 B:384-437 Helix hairpin bin                    CATH domains
               Pfam domains --Tubulin-1tubB01 B:3-226                                                                                                                                                                                                       ------------------------------------Tubulin_C-1tubB02 B:263-393                                                                                                -------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhh.......................................eeeeee...hhhhhh.............eeee..............hhhhhhhhhhhhhhhhh......eeeeeee.....hhhhhhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhh......eeeee.hhhhhhhhhh.........hhhhhhhhhhhhhhh............hhhhhhhh......eeeeeeee..............hhhhhhhh..................eeeeeee....hhhhhhhhhhhhh.............eeeeee........eeeeeeee....hhhhhhhhhhhhh....................hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------V----------S----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE TUBU---------------------------------------------------------------------------------------------------------------------------------------TUBULIN----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tub B   1 MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQD 437
                                    10        20        30        40   ||   52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       370       380       390       400       410       420       430       
                                                                      44|                                                                                                                                                                                                                                                                                                                      360|                                                                    
                                                                       47                                                                                                                                                                                                                                                                                                                       369

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: 60s Ribosomal Protein L30; Chain: A; (235)

Homologous Superfamily: [code=3.30.1330.20, no name defined] (18)

Pig (Sus scrofa) (1)

1a	1tubB02	B:262-383
1b	1tubA02	A:269-383

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1440, no name defined] (23)

Pig (Sus scrofa) (1)

2a	1tubA01	A:1-268
2b	1tubB01	B:1-261

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helix Hairpins (718)

Homologous Superfamily: Helix hairpin bin (5)

Pig (Sus scrofa) (1)

3a	1tubA03	A:384-440
3b	1tubB03	B:384-437

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Tubulin-like (34)

Family: Tubulin (34)

Sus scrofa (Pig) (3)

1a	Tubulin-1tubA01	A:3-226
1b	Tubulin-1tubB01	B:3-226

Family: Tubulin_C (11)

Sus scrofa (Pig) (3)

2a	Tubulin_C-1tubA02	A:263-393
2b	Tubulin_C-1tubB02	B:263-393

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
		Leu B:194 - Val B:195	[ RasMol ]
		Tyr A:357 - Glu A:358	[ RasMol ]

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	1tub
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(no "Related Entries Specified in the PDB File" available for 1TUB)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (6, 6)

PROSITE Motifs (2, 3)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (4, 4)

CATH Domains (3, 6)

Pfam Domains (2, 4)

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