3B6V - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE MOTOR DOMAIN OF HUMAN KINESIN FAMILY MEMBER 3C IN COMPLEX WITH ADP

Authors :   H. Zhu, W. Tempel, Y. Shen, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park, Structural Genomic Consortium (Sgc)

Date :   29 Oct 07 (Deposition) - 13 Nov 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Kinesin, Structural Genomics Consortium, Motor Domain, Adp, Sgc, Atp- Binding, Microtubule, Motor Protein, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Zhu, W. Tempel, Y. Shen, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park
Motor Domain Of Human Kinesin Family Member 3C In Complex With Adp.
To Be Published
PubMed: search

Molecule 1 - KINESIN-LIKE PROTEIN KIF3C
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28-MHP
	Expression System Strain	:	BL21(DE3) CODON(+) RIL
	Expression System Taxid	:	562
	Gene	:	KIF3C
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	UNX	8	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	UNX	3	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 2 (2, 6)

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

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:104 , ADP A:1001 , HOH A:1006 , HOH A:1007 , HOH A:1008	BINDING SITE FOR RESIDUE MG A 1002
02	AC2	SOFTWARE	THR B:104 , ADP B:1001 , HOH B:1008 , HOH B:1009 , HOH B:1010 , HOH B:1013	BINDING SITE FOR RESIDUE MG B 1002
03	AC3	SOFTWARE	ARG A:18 , GLN A:98 , THR A:99 , GLY A:100 , THR A:101 , GLY A:102 , LYS A:103 , THR A:104 , TYR A:105 , THR A:110 , MG A:1002 , HOH A:1006 , HOH A:1008 , TRP B:111	BINDING SITE FOR RESIDUE ADP A 1001
04	AC4	SOFTWARE	ASP A:65 , ALA A:66	BINDING SITE FOR RESIDUE UNX A 1003
05	AC5	SOFTWARE	GLY A:331 , GLY A:332	BINDING SITE FOR RESIDUE UNX A 1004
06	AC6	SOFTWARE	TYR A:105 , THR A:110 , TRP A:111 , LEU A:116	BINDING SITE FOR RESIDUE UNX A 1005
07	AC7	SOFTWARE	TRP A:111 , ARG B:18 , PRO B:19 , GLN B:98 , THR B:99 , GLY B:100 , THR B:101 , GLY B:102 , LYS B:103 , THR B:104 , TYR B:105 , THR B:110 , MG B:1002 , HOH B:1008 , HOH B:1013	BINDING SITE FOR RESIDUE ADP B 1001
08	AC8	SOFTWARE	TYR B:96 , GLY B:97 , ALA B:248 , SER B:250	BINDING SITE FOR RESIDUE UNX B 1003
09	AC9	SOFTWARE	ARG B:16 , GLN B:70 , THR B:106 , GLY B:118 , VAL B:119	BINDING SITE FOR RESIDUE UNX B 1004
10	BC1	SOFTWARE	ARG B:324 , LEU B:325 , GLN B:327 , ASP B:328	BINDING SITE FOR RESIDUE UNX B 1005
11	BC2	SOFTWARE	LYS B:56 , ARG B:357	BINDING SITE FOR RESIDUE UNX B 1006
12	BC3	SOFTWARE	ALA B:10 , LYS B:335 , THR B:336	BINDING SITE FOR RESIDUE UNX B 1007

(no "SS Bond" information available for 3B6V)

(no "Cis Peptide Bond" information available for 3B6V)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_055120	Q	370	R	KIF3C_HUMAN	Polymorphism	1465878	A/B	R	370	R

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_055120	Q	370	R	KIF3C_HUMAN	Polymorphism	1465878	A	R	370	R

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_055120	Q	370	R	KIF3C_HUMAN	Polymorphism	1465878	B	R	370	R

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KINESIN_MOTOR_2	PS50067	Kinesin motor domain profile.	KIF3C_HUMAN	10-365	2	A:10-365 B:10-365
2	KINESIN_MOTOR_1	PS00411	Kinesin motor domain signature.	KIF3C_HUMAN	240-251	2	A:240-251 B:240-251

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KINESIN_MOTOR_2	PS50067	Kinesin motor domain profile.	KIF3C_HUMAN	10-365	1	A:10-365 -
2	KINESIN_MOTOR_1	PS00411	Kinesin motor domain signature.	KIF3C_HUMAN	240-251	1	A:240-251 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KINESIN_MOTOR_2	PS50067	Kinesin motor domain profile.	KIF3C_HUMAN	10-365	1	- B:10-365
2	KINESIN_MOTOR_1	PS00411	Kinesin motor domain signature.	KIF3C_HUMAN	240-251	1	- B:240-251

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000264712	1b	ENSE00001753692	chr2:26205366-26203242	2125	KIF3C_HUMAN	1-515	515	2	A:8-381 (gaps) B:7-372 (gaps)	374 366
1.2a	ENST00000264712	2a	ENSE00000808974	chr2:26179313-26179212	102	KIF3C_HUMAN	516-549	34	0	-	-
1.3	ENST00000264712	3	ENSE00000808973	chr2:26178532-26178410	123	KIF3C_HUMAN	550-590	41	0	-	-
1.4a	ENST00000264712	4a	ENSE00000808972	chr2:26177254-26177136	119	KIF3C_HUMAN	591-630	40	0	-	-
1.5b	ENST00000264712	5b	ENSE00000962985	chr2:26174774-26174658	117	KIF3C_HUMAN	630-669	40	0	-	-
1.8a	ENST00000264712	8a	ENSE00001654042	chr2:26152932-26152824	109	KIF3C_HUMAN	669-705	37	0	-	-
1.9b	ENST00000264712	9b	ENSE00001642007	chr2:26152346-26152174	173	KIF3C_HUMAN	706-763	58	0	-	-
1.10b	ENST00000264712	10b	ENSE00001078122	chr2:26151940-26149471	2470	KIF3C_HUMAN	763-793	31	0	-	-

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:306
 aligned with KIF3C_HUMAN | O14782 from UniProtKB/Swiss-Prot  Length:793

    Alignment length:374
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377    
          KIF3C_HUMAN     8 SEALKVVARCRPLSRKEEAAGHEQILTMDVKLGQVTLRNPRAAPGELPKTFTFDAVYDASSKQADLYDETVRPLIDSVLQGFNGTVFAYGQTGTGKTYTMQGTWVEPELRGVIPNAFEHIFTHISRSQNQQYLVRASYLEIYQEEIRDLLSKEPGKRLELKENPETGVYIKDLSSFVTKNVKEIEHVMNLGNQTRAVGSTHMNEVSSRSHAIFIITVECSERGSDGQDHIRVGKLNLVDLAGSERQNKAGPNTAGGAATPSSGGGGGGGGSGGGAGGERPKEASKINLSLSALGNVIAALAGNRSTHIPYRDSKLTRLLQDSLGGNAKTIMVATLGPASHSYDESLSTLRFANRAKNIKNKPQVNEDPKDTLLR 381
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b6vA00 A:8-381 Kinesin                                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.eeeeee...hhhhhhh.....eeee....eeee...........eeee..eee....hhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhh.........hhhhhhhhhhhhhhhhh...eeeeeeeeeee....eee...----.ee.eeee...eeee.....ee..hhhhhhhhhhhhhhhh----------....eeeeeeeeeee.-------..eeeeeeeee.....------------------------------------------hhhhhhhhhhhhhhh-----..hhhhhhhhhhhhhhh....eeeeeeee..hhhhhhhhhhhhhhhhhhh..ee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------- SAPs(SNPs)
                PROSITE (1) --KINESIN_MOTOR_2  PDB: A:10-365 UniProt: 10-365                                                                                                                                                                                                                                                                                                                      ---------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO---------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1b  PDB: A:8-381 (gaps) UniProt: 1-515 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                             Transcript 1
                 3b6v A   8 SEALKVVARCRPLSRKEEAAGHEQILTMDVKLGQVTLRNPRAAPGELPKTFTFDAVYDASSKQADLYDETVRPLIDSVLQGFNGTVFAYGQTGTGKTYTMQGTWVEPELRGVIPNAFEHIFTHISRSQNQQYLVRASYLEIYQEEIRDLLS----KRLELKENPETGVYIKDLSSFVTKNVKEIEHVMNLGNQTR----------SSRSHAIFIITVECSE-------HIRVGKLNLVDLAGSE------------------------------------------NLSLSALGNVIAALA-----HIPYRDSKLTRLLQDSLGGNAKTIMVATLGPASHSYDESLSTLRFANRAKNIKNKPRVNEDPKDTLLR 381
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157|    | 167       177       187       197    |    -     | 217       227|      237       247   |     -         -         -         -      |297       307|     |317       327       337       347       357       367       377    
                                                                                                                                                                                158  163                                    202        213            228     236            251                                        294           308   314

Chain B from PDB  Type:PROTEIN  Length:302
 aligned with KIF3C_HUMAN | O14782 from UniProtKB/Swiss-Prot  Length:793

    Alignment length:366
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366      
          KIF3C_HUMAN     7 ASEALKVVARCRPLSRKEEAAGHEQILTMDVKLGQVTLRNPRAAPGELPKTFTFDAVYDASSKQADLYDETVRPLIDSVLQGFNGTVFAYGQTGTGKTYTMQGTWVEPELRGVIPNAFEHIFTHISRSQNQQYLVRASYLEIYQEEIRDLLSKEPGKRLELKENPETGVYIKDLSSFVTKNVKEIEHVMNLGNQTRAVGSTHMNEVSSRSHAIFIITVECSERGSDGQDHIRVGKLNLVDLAGSERQNKAGPNTAGGAATPSSGGGGGGGGSGGGAGGERPKEASKINLSLSALGNVIAALAGNRSTHIPYRDSKLTRLLQDSLGGNAKTIMVATLGPASHSYDESLSTLRFANRAKNIKNKPQVN 372
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3b6vB00 B:7-372 Kinesin                                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.eeeeee...hhhhhhh.....eeee....eeee...........eeee..eee....hhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhh.........hhhhhhhhhhhhhhhh....eeeeeeeeeeee..eeee........ee.ee.----..ee.....eee.hhhhhhhhhhhhhhhh--------......eeeeeeeeeee.-------..eeeeeeeee.....----------------------------------------..hhhhhhhhhhhhhhh-----..hhhhhhhhhhh........eeeeeeee..hhhhhhhhhhhhhhhhhhh..ee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R-- SAPs(SNPs)
                PROSITE (1) ---KINESIN_MOTOR_2  PDB: B:10-365 UniProt: 10-365                                                                                                                                                                                                                                                                                                                      ------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1b  PDB: B:7-372 (gaps) UniProt: 1-515 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                     Transcript 1
                 3b6v B   7 ASEALKVVARCRPLSRKEEAAGHEQILTMDVKLGQVTLRNPRAAPGELPKTFTFDAVYDASSKQADLYDETVRPLIDSVLQGFNGTVFAYGQTGTGKTYTMQGTWVEPELRGVIPNAFEHIFTHISRSQNQQYLVRASYLEIYQEEIRDLLSKEPGKRLELKE----GVYIKDLSSFVTKNVKEIEHVMNLGNQTR--------EVSSRSHAIFIITVECSE-------HIRVGKLNLVDLAGSE----------------------------------------KINLSLSALGNVIAALA-----HIPYRDSKLTRLLQDSLGGNAKTIMVATLGPASHSYDESLSTLRFANRAKNIKNKPRVN 372
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166  |    176       186       196     |   -    |  216       226 |     236       246    |    -         -         -         -     | 296       306 |     316       326       336       346       356       366      
                                                                                                                                                                                            169  174                         202      211              228     236            251                                      292             308   314

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 3B6V)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Kinesin (69)

Homologous Superfamily: Kinesin (69)

Human (Homo sapiens) (36)

1a	3b6vA00	A:8-381
1b	3b6vB00	B:7-372

(no "Pfam Domain" information available for 3B6V)

Asymmetric Unit(hide GO term definitions)

Chain A,B (KIF3C_HUMAN | O14782)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0008017	microtubule binding	Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
	GO:0003777	microtubule motor activity	Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).
	GO:0003774	motor activity	Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate.
	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.
biological process
	GO:0019886	antigen processing and presentation of exogenous peptide antigen via MHC class II	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
	GO:0007018	microtubule-based movement	A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
	GO:0072384	organelle transport along microtubule	The directed movement of an organelle along a microtubule, mediated by motor proteins. This process begins with the attachment of an organelle to a microtubule, and ends when the organelle reaches its final destination.
	GO:0006890	retrograde vesicle-mediated transport, Golgi to ER	The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.
cellular component
	GO:0097542	ciliary tip	Part of the cilium where the axoneme ends. The ciliary tip has been implicated in ciliary assembly and disassembly, as well as signal transduction.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005871	kinesin complex	Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work.
	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.

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3b6u	CRYSTAL STRUCTURE OF MOTOR DOMAIN OF HUMAN KINESIN FAMILY MEMBER 3B IN COMPLEX WITH ADP

Description

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Ligands, Modified Residues, Ions (3, 12)

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SS Bonds (0, 0)

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Sequence-Structure Mapping

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Exons (1, 2)

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