3T5D - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF SEPTIN 7 IN COMPLEX WITH GDP

Authors :   E. Zent, A. Wittinghofer

Date :   27 Jul 11 (Deposition) - 24 Aug 11 (Release) - 24 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

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

Keywords :   Gtp-Binding Protein, Cytoskeleton, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Zent, I. Vetter, A. Wittinghofer
Structural And Biochemical Properties Of Sept7, A Unique Septin Required For Filament Formation.
Biol. Chem. V. 392 791 2011
PubMed-ID: 21824007 | Reference-DOI: 10.1515/BC.2011.082

Molecule 1 - SEPTIN-7
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	SEPT7, CDC10
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CDC10 PROTEIN HOMOLOG

		1	2
Asymmetric/Biological Unit	:	A	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:41 , LEU A:42 , GLY A:43 , LYS A:44 , SER A:45 , THR A:46 , LYS A:176 , ASP A:178 , VAL A:230 , GLY A:231 , ARG A:246 , TYR A:248 , SER C:149 , HIS C:151 , THR C:179 , GLU C:184	BINDING SITE FOR RESIDUE GDP A 1
2	AC2	SOFTWARE	SER A:149 , HIS A:151 , THR A:179 , GLU A:184 , GLY C:41 , LEU C:42 , GLY C:43 , LYS C:44 , SER C:45 , THR C:46 , LYS C:176 , ASP C:178 , VAL C:230 , GLY C:231 , ARG C:246 , TYR C:248	BINDING SITE FOR RESIDUE GDP C 1

(no "SS Bond" information available for 3T5D)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:97	-	Phe A:98
2	Gly A:99	-	Asp A:100
3	Asp A:100	-	Ala A:101
4	Val A:102	-	Asp A:103
5	Pro A:148	-	Ser A:149
6	Ser A:149	-	Gly A:150
7	Gly A:150	-	His A:151
8	Leu A:225	-	Pro A:226
9	Lys C:69	-	Lys C:70
10	Thr C:71	-	Val C:72
11	Gly C:97	-	Phe C:98
12	Gly C:99	-	Asp C:100
13	Asp C:100	-	Ala C:101
14	Val C:102	-	Asp C:103
15	Pro C:148	-	Ser C:149
16	Ser C:149	-	Gly C:150
17	Gly C:150	-	His C:151
18	Leu C:225	-	Pro C:226

(no "SAP(SNP)/Variant" information available for 3T5D)

(no "PROSITE Motif" information available for 3T5D)

Asymmetric/Biological Unit (9, 18)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000350320	1c	ENSE00001745473	chr7:35840627-35840882	256	SEPT7_HUMAN	1-21	21	0	-	-
1.5c	ENST00000350320	5c	ENSE00001656934	chr7:35872408-35872510	103	SEPT7_HUMAN	22-56	35	2	A:30-37 C:30-37	8 8
1.6	ENST00000350320	6	ENSE00001751801	chr7:35903162-35903268	107	SEPT7_HUMAN	56-91	36	2	A:37-72 (gaps) C:37-72 (gaps)	36 36
1.7	ENST00000350320	7	ENSE00001618039	chr7:35912276-35912376	101	SEPT7_HUMAN	92-125	34	2	A:73-106 (gaps) C:73-106 (gaps)	34 34
1.8a	ENST00000350320	8a	ENSE00001661190	chr7:35913251-35913385	135	SEPT7_HUMAN	125-170	46	2	A:106-151 C:106-151	46 46
1.10	ENST00000350320	10	ENSE00001622608	chr7:35919433-35919550	118	SEPT7_HUMAN	170-209	40	2	A:151-190 C:151-190	40 40
1.11	ENST00000350320	11	ENSE00001263591	chr7:35922094-35922186	93	SEPT7_HUMAN	210-240	31	2	A:191-221 (gaps) C:191-221 (gaps)	31 31
1.12	ENST00000350320	12	ENSE00001606979	chr7:35923501-35923597	97	SEPT7_HUMAN	241-273	33	2	A:222-254 (gaps) C:222-254 (gaps)	33 33
1.13	ENST00000350320	13	ENSE00001677112	chr7:35925438-35925489	52	SEPT7_HUMAN	273-290	18	2	A:254-271 C:254-271	18 18
1.14b	ENST00000350320	14b	ENSE00000832354	chr7:35930278-35930403	126	SEPT7_HUMAN	290-332	43	2	A:271-297 C:271-297	27 27
1.16b	ENST00000350320	16b	ENSE00001662836	chr7:35937858-35937993	136	SEPT7_HUMAN	332-377	46	0	-	-
1.16f	ENST00000350320	16f	ENSE00000832356	chr7:35942686-35942825	140	SEPT7_HUMAN	378-424	47	0	-	-
1.17a	ENST00000350320	17a	ENSE00001712469	chr7:35943864-35944915	1052	SEPT7_HUMAN	424-436	13	0	-	-

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:232
 aligned with SEPT7_HUMAN | Q16181 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:268
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308        
          SEPT7_HUMAN    49 FEFTLMVVGESGLGKSTLINSLFLTDLYSPEYPGPSHRIKKTVQVEQSKVLIKEGGVQLLLTIVDTPGFGDAVDNSNCWQPVIDYIDSKFEDYLNAESRVNRRQMPDNRVQCCLYFIAPSGHGLKPLDIEFMKRLHEKVNIIPLIAKADTLTPEECQQFKKQIMKEIQEHKIKIYEFPETDDEEENKLVKKIKDRLPLAVVGSNTIIEVNGKRVRGRQYPWGVAEVENGEHCDFTILRNMLIRTHMQDLKDVTNNVHYENYRSRKLAA 316
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhh....---------------...eeeeeee..--..eeeeeee.............hhhhhhhhhhhhhhhhhhhhh............eeeeee.......hhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......-----------hhhhhhh..ee.......--------.eee....eee.......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.5c    -----------------------------------Exon 1.7  PDB: A:73-106 (gaps)    --------------------------------------------Exon 1.10  PDB: A:151-190               Exon 1.11  PDB: A:191-221 (gapsExon 1.12  PDB: A:222-254 (gaps) ----------------Exon 1.14b  PDB: A:271-297  Transcript 1 (1)
           Transcript 1 (2) -------Exon 1.6  PDB: A:37-72 (gaps)       ---------------------------------Exon 1.8a  PDB: A:106-151 UniProt: 125-170    ------------------------------------------------------------------------------------------------------Exon 1.13         -------------------------- Transcript 1 (2)
                 3t5d A  30 FEFTLMVVGESGLGKSTLINSLFLTDL---------------VQVEQSKVLIKE--VQLLLTIVDTPGFGDAVDNSNCWQPVIDYIDSKFEDYLNAESRVNRRQMPDNRVQCCLYFIAPSGHGLKPLDIEFMKRLHEKVNIIPLIAKADTLTPEECQQFKKQIMKEIQEHKIKIYEF-----------VKKIKDRLPLAVVGSNTI--------RGRQYPWGVAEVENGEHCDFTILRNMLIRTHMQDLKDVTNNVHYENYRSRKLAA 297
                                    39        49      |  -         -  |     79   |  | 89        99       109       119       129       139       149       159       169       179       189       199      |  -       219       229     |   -    |  249       259       269       279       289        
                                                     56              72         83 86                                                                                                                     206         218              235      244

Chain C from PDB  Type:PROTEIN  Length:235
 aligned with SEPT7_HUMAN | Q16181 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:268
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308        
          SEPT7_HUMAN    49 FEFTLMVVGESGLGKSTLINSLFLTDLYSPEYPGPSHRIKKTVQVEQSKVLIKEGGVQLLLTIVDTPGFGDAVDNSNCWQPVIDYIDSKFEDYLNAESRVNRRQMPDNRVQCCLYFIAPSGHGLKPLDIEFMKRLHEKVNIIPLIAKADTLTPEECQQFKKQIMKEIQEHKIKIYEFPETDDEEENKLVKKIKDRLPLAVVGSNTIIEVNGKRVRGRQYPWGVAEVENGEHCDFTILRNMLIRTHMQDLKDVTNNVHYENYRSRKLAA 316
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhh....-----------.......eeeeeee..--..eeeeeee.............hhhhhhhhhhhhhhhhhhhhh............eeeeee.......hhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.....------------hhhhhhhh..ee.......--------.eee....eee.......hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.5c    -----------------------------------Exon 1.7  PDB: C:73-106 (gaps)    --------------------------------------------Exon 1.10  PDB: C:151-190               Exon 1.11  PDB: C:191-221 (gapsExon 1.12  PDB: C:222-254 (gaps) ----------------Exon 1.14b  PDB: C:271-297  Transcript 1 (1)
           Transcript 1 (2) -------Exon 1.6  PDB: C:37-72 (gaps)       ---------------------------------Exon 1.8a  PDB: C:106-151 UniProt: 125-170    ------------------------------------------------------------------------------------------------------Exon 1.13         -------------------------- Transcript 1 (2)
                 3t5d C  30 FEFTLMVVGESGLGKSTLINSLFLTDL-----------IKKTVQVEQSKVLIKE--VQLLLTIVDTPGFGDAVDNSNCWQPVIDYIDSKFEDYLNAESRVNRRQMPDNRVQCCLYFIAPSGHGLKPLDIEFMKRLHEKVNIIPLIAKADTLTPEECQQFKKQIMKEIQEHKIKIY------------LVKKIKDRLPLAVVGSNTI--------RGRQYPWGVAEVENGEHCDFTILRNMLIRTHMQDLKDVTNNVHYENYRSRKLAA 297
                                    39        49      |  -        69        79   |  | 89        99       109       119       129       139       149       159       169       179       189       199    |    -       219       229     |   -    |  249       259       269       279       289        
                                                     56          68             83 86                                                                                                                   204          217               235      244

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 3T5D)

(no "CATH Domain" information available for 3T5D)

(no "Pfam Domain" information available for 3T5D)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (SEPT7_HUMAN | Q16181)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0060271	cilium assembly	The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
	GO:0000910	cytokinesis	The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
	GO:1902857	positive regulation of non-motile cilium assembly	Any process that activates or increases the frequency, rate or extent of non-motile cilium assembly.
	GO:0051291	protein heterooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0016476	regulation of embryonic cell shape	Any process that modulates the surface configuration of an embryonic cell.
cellular component
	GO:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0016324	apical plasma membrane	The region of the plasma membrane located at the apical end of the cell.
	GO:0005930	axoneme	The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000775	chromosome, centromeric region	The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	GO:0005929	cilium	A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
	GO:0032154	cleavage furrow	The cleavage furrow is a plasma membrane invagination at the cell division site. The cleavage furrow begins as a shallow groove and eventually deepens to divide the cytoplasm.
	GO:0000777	condensed chromosome kinetochore	A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0000776	kinetochore	A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
	GO:0015630	microtubule cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
	GO:0030496	midbody	A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0031105	septin complex	A protein complex containing septins. Typically, these complexes contain multiple septins and are oligomeric.
	GO:0005819	spindle	The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.
	GO:0001725	stress fiber	A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp A:100 - Ala A:101	[ RasMol ]
		Asp C:100 - Ala C:101	[ RasMol ]
		Gly A:150 - His A:151	[ RasMol ]
		Gly A:97 - Phe A:98	[ RasMol ]
		Gly A:99 - Asp A:100	[ RasMol ]
		Gly C:150 - His C:151	[ RasMol ]
		Gly C:97 - Phe C:98	[ RasMol ]
		Gly C:99 - Asp C:100	[ RasMol ]
		Leu A:225 - Pro A:226	[ RasMol ]
		Leu C:225 - Pro C:226	[ RasMol ]
		Lys C:69 - Lys C:70	[ RasMol ]
		Pro A:148 - Ser A:149	[ RasMol ]
		Pro C:148 - Ser C:149	[ RasMol ]
		Ser A:149 - Gly A:150	[ RasMol ]
		Ser C:149 - Gly C:150	[ RasMol ]
		Thr C:71 - Val C:72	[ RasMol ]
		Val A:102 - Asp A:103	[ RasMol ]
		Val C:102 - Asp C:103	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3T5D)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (18, 18)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (9, 18)

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