2QFZ - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN TBC1 DOMAIN FAMILY MEMBER 22A

Authors :   Y. Tong, W. Tempel, S. Dimov, A. Dong, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)

Date :   28 Jun 07 (Deposition) - 10 Jul 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Rab-Gap, Gtpase Activator, Tbc1, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase Activator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Tong, W. Tempel, S. Dimov, A. Dong, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of Human Tbc1 Domain Family Member 22A.
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - TBC1 DOMAIN FAMILY MEMBER 22A
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A-MHL
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TBC1D22A, C22ORF4
	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 (1, 12)

No.	Name	Count	Type	Full Name
1	UNX	12	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (1, 7)

No.	Name	Count	Type	Full Name
1	UNX	7	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	UNX	5	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:375 , GLU A:471 , GLU A:476	BINDING SITE FOR RESIDUE UNX A 1001
02	AC2	SOFTWARE	ARG B:420 , ASN B:424 , LEU B:426 , MET B:427 , ARG B:428 , GLU B:429	BINDING SITE FOR RESIDUE UNX B 1002
03	AC3	SOFTWARE	GLN B:416 , PHE B:417 , PHE B:419 , ARG B:420	BINDING SITE FOR RESIDUE UNX B 1003
04	AC4	SOFTWARE	ARG A:420 , TRP A:421 , ASN A:424 , LEU A:426 , MET A:427 , ARG A:428 , GLU A:429	BINDING SITE FOR RESIDUE UNX A 1004
05	AC5	SOFTWARE	PHE B:449 , SER B:450 , HOH B:2028 , HOH B:2046	BINDING SITE FOR RESIDUE UNX B 1005
06	AC6	SOFTWARE	PHE A:417 , ARG A:420 , TRP A:421	BINDING SITE FOR RESIDUE UNX A 1006
07	AC7	SOFTWARE	PHE A:449 , SER A:450 , HOH A:2041	BINDING SITE FOR RESIDUE UNX A 1007
08	AC8	SOFTWARE	ASP A:493 , LEU A:496 , LEU A:497	BINDING SITE FOR RESIDUE UNX A 1008
09	AC9	SOFTWARE	ARG A:217 , SER A:221	BINDING SITE FOR RESIDUE UNX A 1009
10	BC1	SOFTWARE	ARG B:433	BINDING SITE FOR RESIDUE UNX B 1010
11	BC2	SOFTWARE	ASP A:408 , HOH A:2066 , ASP B:283 , GLN B:320 , HOH B:2052 , HOH B:2069	BINDING SITE FOR RESIDUE UNX B 1011
12	BC3	SOFTWARE	ASP A:283 , GLN A:320 , ASP B:408	BINDING SITE FOR RESIDUE UNX A 1012

(no "SS Bond" information available for 2QFZ)

Asymmetric Unit

No.	Residues
1	Gly A:207	-	Pro A:208
2	Ser A:288	-	Pro A:289
3	Gly B:207	-	Pro B:208
4	Ser B:288	-	Pro B:289

(no "SAP(SNP)/Variant" information available for 2QFZ)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TBC_RABGAP	PS50086	TBC/rab GAP domain profile.	TB22A_HUMAN	222-446	2	A:222-446 B:222-446

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TBC_RABGAP	PS50086	TBC/rab GAP domain profile.	TB22A_HUMAN	222-446	1	A:222-446 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TBC_RABGAP	PS50086	TBC/rab GAP domain profile.	TB22A_HUMAN	222-446	1	- B:222-446

Asymmetric Unit (10, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000337137	1a	ENSE00001916547	chr22:47158518-47158745	228	TB22A_HUMAN	1-21	21	0	-	-
1.8	ENST00000337137	8	ENSE00001771548	chr22:47188417-47188473	57	TB22A_HUMAN	21-40	20	0	-	-
1.10e	ENST00000337137	10e	ENSE00001669083	chr22:47189398-47189738	341	TB22A_HUMAN	40-154	115	0	-	-
1.11	ENST00000337137	11	ENSE00001145595	chr22:47193341-47193517	177	TB22A_HUMAN	154-213	60	2	A:196-213 B:196-213	18 18
1.12	ENST00000337137	12	ENSE00001145586	chr22:47274549-47274619	71	TB22A_HUMAN	213-236	24	2	A:213-236 B:213-236	24 24
1.13	ENST00000337137	13	ENSE00001711751	chr22:47287162-47287290	129	TB22A_HUMAN	237-279	43	2	A:237-279 (gaps) B:237-279 (gaps)	43 43
1.14	ENST00000337137	14	ENSE00001780399	chr22:47290680-47290742	63	TB22A_HUMAN	280-300	21	2	A:280-300 B:280-300	21 21
1.15	ENST00000337137	15	ENSE00001690383	chr22:47307970-47308084	115	TB22A_HUMAN	301-339	39	2	A:301-339 B:301-339	39 39
1.17	ENST00000337137	17	ENSE00001792267	chr22:47370186-47370295	110	TB22A_HUMAN	339-375	37	2	A:339-375 (gaps) B:339-375 (gaps)	37 37
1.18	ENST00000337137	18	ENSE00001677535	chr22:47393530-47393605	76	TB22A_HUMAN	376-401	26	2	A:376-401 B:376-401	26 26
1.19	ENST00000337137	19	ENSE00001612992	chr22:47432967-47433094	128	TB22A_HUMAN	401-443	43	2	A:401-443 B:401-443	43 43
1.20	ENST00000337137	20	ENSE00001743071	chr22:47507404-47507499	96	TB22A_HUMAN	444-475	32	2	A:444-475 B:444-475	32 32
1.21e	ENST00000337137	21e	ENSE00001936582	chr22:47569141-47571336	2196	TB22A_HUMAN	476-517	42	2	A:476-508 B:476-507	33 32

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:300
 aligned with TB22A_HUMAN | Q8WUA7 from UniProtKB/Swiss-Prot  Length:517

    Alignment length:313
                                   205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505   
          TB22A_HUMAN   196 SRLDKFKQLLAGPNTDLEELRRLSWSGIPKPVRPMTWKLLSGYLPANVDRRPATLQRKQKEYFAFIEHYYDSRNDEVHQDTYRQIHIDIPRMSPEALILQPKVTEIFERILFIWAIRHPASGYVQGINDLVTPFFVVFICEYIEAEEVDTVDVSGVPAEVLCNIEADTYWCMSKLLDGIQDNYTFAQPGIQMKVKMLEELVSRIDEQVHRHLDQHEVRYLQFAFRWMNNLLMREVPLRCTIRLWDTYQSEPDGFSHFHLYVCAAFLVRWRKEILEEKDFQELLLFLQNLPTAHWDDEDISLLLAEAYRLKFAF 508
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh--------hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.-----.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------TBC_RABGAP  PDB: A:222-446 UniProt: 222-446                                                                                                                                                                                      -------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11         -----------------------Exon 1.13  PDB: A:237-279 (gaps)           Exon 1.14            Exon 1.15  PDB: A:301-339              ------------------------------------Exon 1.18  PDB: A:376-401 ------------------------------------------Exon 1.20  PDB: A:444-475       Exon 1.21e  PDB: A:476-508        Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.12  PDB: A:213-23------------------------------------------------------------------------------------------------------Exon 1.17  PDB: A:339-375 (gaps)     -------------------------Exon 1.19  PDB: A:401-443 UniProt: 401-443 ----------------------------------------------------------------- Transcript 1 (2)
                 2qfz A 196 SRLDKFKQLLAGPNTDLEELRRLSWSGIPKPVRPMTWKLLSGYLPANVDRRPATLQRKQKEYFAFIEHY--------HQDTYRQIHIDIPRMSPEALILQPKVTEIFERILFIWAIRHPASGYVQGINDLVTPFFVVFICEYIE-----TVDVSGVPAEVLCNIEADTYWCMSKLLDGIQDNYTFAQPGIQMKVKMLEELVSRIDEQVHRHLDQHEVRYLQFAFRWMNNLLMREVPLRCTIRLWDTYQSEPDGFSHFHLYVCAAFLVRWRKEILEEKDFQELLLFLQNLPTAHWDDEDISLLLAEAYRLKFAF 508
                                   205       215       225       235       245       255        |-       275       285       295       305       315       325       335   |   345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505   
                                                                                              264      273                                                               339   345

Chain B from PDB  Type:PROTEIN  Length:299
 aligned with TB22A_HUMAN | Q8WUA7 from UniProtKB/Swiss-Prot  Length:517

    Alignment length:312
                                   205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505  
          TB22A_HUMAN   196 SRLDKFKQLLAGPNTDLEELRRLSWSGIPKPVRPMTWKLLSGYLPANVDRRPATLQRKQKEYFAFIEHYYDSRNDEVHQDTYRQIHIDIPRMSPEALILQPKVTEIFERILFIWAIRHPASGYVQGINDLVTPFFVVFICEYIEAEEVDTVDVSGVPAEVLCNIEADTYWCMSKLLDGIQDNYTFAQPGIQMKVKMLEELVSRIDEQVHRHLDQHEVRYLQFAFRWMNNLLMREVPLRCTIRLWDTYQSEPDGFSHFHLYVCAAFLVRWRKEILEEKDFQELLLFLQNLPTAHWDDEDISLLLAEAYRLKFA 507
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------RabGAP-TBC-2qfzB01 B:225-469                                                                                                                                                                                                                         -------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------RabGAP-TBC-2qfzB02 B:225-469                                                                                                                                                                                                                         -------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh-------hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...------......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------TBC_RABGAP  PDB: B:222-446 UniProt: 222-446                                                                                                                                                                                      ------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11         -----------------------Exon 1.13  PDB: B:237-279 (gaps)           Exon 1.14            Exon 1.15  PDB: B:301-339              ------------------------------------Exon 1.18  PDB: B:376-401 ------------------------------------------Exon 1.20  PDB: B:444-475       Exon 1.21e  PDB: B:476-507       Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.12  PDB: B:213-23------------------------------------------------------------------------------------------------------Exon 1.17  PDB: B:339-375 (gaps)     -------------------------Exon 1.19  PDB: B:401-443 UniProt: 401-443 ---------------------------------------------------------------- Transcript 1 (2)
                 2qfz B 196 SRLDKFKQLLAGPNTDLEELRRLSWSGIPKPVRPMTWKLLSGYLPANVDRRPATLQRKQKEYFAFIEHYY-------HQDTYRQIHIDIPRMSPEALILQPKVTEIFERILFIWAIRHPASGYVQGINDLVTPFFVVFICEYIE------VDVSGVPAEVLCNIEADTYWCMSKLLDGIQDNYTFAQPGIQMKVKMLEELVSRIDEQVHRHLDQHEVRYLQFAFRWMNNLLMREVPLRCTIRLWDTYQSEPDGFSHFHLYVCAAFLVRWRKEILEEKDFQELLLFLQNLPTAHWDDEDISLLLAEAYRLKFA 507
                                   205       215       225       235       245       255       265       275       285       295       305       315       325       335   |     -|      355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505  
                                                                                               265     273                                                               339    346

Legend:		→ Mismatch	(orange background)
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		→ 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 2QFZ)

(no "CATH Domain" information available for 2QFZ)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: RabGAP-TBC] (5)

Family: RabGAP-TBC (5)

Homo sapiens (Human) (5)

1a	RabGAP-TBC-2qfzB01	B:225-469
1b	RabGAP-TBC-2qfzB02	B:225-469

Asymmetric Unit(hide GO term definitions)

Chain A,B (TB22A_HUMAN | Q8WUA7)

molecular function
	GO:0071889	14-3-3 protein binding	Interacting selectively and non-covalently with a 14-3-3 protein. A 14-3-3 protein is any of a large family of approximately 30kDa acidic proteins which exist primarily as homo- and heterodimers within all eukaryotic cells, and have been implicated in the modulation of distinct biological processes by binding to specific phosphorylated sites on diverse target proteins, thereby forcing conformational changes or influencing interactions between their targets and other molecules. Each 14-3-3 protein sequence can be roughly divided into three sections: a divergent amino terminus, the conserved core region and a divergent carboxyl terminus. The conserved middle core region of the 14-3-3s encodes an amphipathic groove that forms the main functional domain, a cradle for interacting with client proteins.
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
	GO:0017137	Rab GTPase binding	Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0090630	activation of GTPase activity	Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
	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:1902017	regulation of cilium assembly	Any process that modulates the frequency, rate or extent of cilium assembly.
	GO:0031338	regulation of vesicle fusion	Any process that modulates the frequency, rate or extent of vesicle fusion.
cellular component
	GO:0012505	endomembrane system	A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric Unit
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	Cis Peptide Bonds
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		Ser A:288 - Pro A:289	[ RasMol ]
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	2qfz
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Description

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Ligands, Modified Residues, Ions (1, 12)

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Cis Peptide Bonds (4, 4)

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