4DXS - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   HUMAN SUN2-KASH2 COMPLEX

Authors :   B. Sosa, T. U. Schwartz

Date :   28 Feb 12 (Deposition) - 06 Jun 12 (Release) - 06 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.71

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

Keywords :   Beta-Sandwich, Linc Complex, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. A. Sosa, A. Rothballer, U. Kutay, T. U. Schwartz
Linc Complexes Form By Binding Of Three Kash Peptides To Domain Interfaces Of Trimeric Sun Proteins.
Cell(Cambridge, Mass. ) V. 149 1035 2012
PubMed-ID: 22632968 | Reference-DOI: 10.1016/J.CELL.2012.03.046

Molecule 1 - SUN DOMAIN-CONTAINING PROTEIN 2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	SUN DOMAIN (UNP RESIDUES 522-717)
	Gene	:	SUN2, FRIGG, KIAA0668, RAB5IP, UNC84B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN UNC-84 HOMOLOG B, RAB5-INTERACTING PROTEIN, RAB5IP, SAD1/UNC-84 PROTEIN-LIKE 2

Molecule 2 - NESPRIN-2
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 6857-6885
	Gene	:	SYNE2, KIAA1011, NUA
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NUCLEAR ENVELOPE SPECTRIN REPEAT PROTEIN 2, NUCLEUS AND ACTIN CONNECTING ELEMENT PROTEIN, PROTEIN NUANCE, SYNAPTIC NUCLEAR ENVELOPE PROTEIN 2, SYNE-2

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	DMU	1	Ligand/Ion	DECYL-BETA-D-MALTOPYRANOSIDE
2	K	1	Ligand/Ion	POTASSIUM ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	DMU	3	Ligand/Ion	DECYL-BETA-D-MALTOPYRANOSIDE
2	K	-1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:552 , SER A:553 , LEU A:574 , TRP A:582 , GLN A:586 , ARG A:589 , ASN A:600 , HOH A:935 , TYR B:6878	BINDING SITE FOR RESIDUE DMU A 801
2	AC2	SOFTWARE	VAL A:590 , GLN A:593 , ASP A:595 , ASN A:600 , TYR A:707	BINDING SITE FOR RESIDUE K A 802

Asymmetric Unit

No.	Residues
1	A:563	-	B:6862
2	A:601	-	A:705

(no "Cis Peptide Bond" information available for 4DXS)

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024624	G	671	S	SUN2_HUMAN	Polymorphism	2072797	A	G	671	S

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

Biological Unit 1 (1, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024624	G	671	S	SUN2_HUMAN	Polymorphism	2072797	A	G	671	S

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SUN	PS51469	SUN domain profile.	SUN2_HUMAN	555-716	1	A:555-716

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SUN	PS51469	SUN domain profile.	SUN2_HUMAN	555-716	3	A:555-716

(no "Exon" information available for 4DXS)

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:196
 aligned with SUN2_HUMAN | Q9UH99 from UniProtKB/Swiss-Prot  Length:717

    Alignment length:196
                                   531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711      
          SUN2_HUMAN    522 GVTEEQVHHIVKQALQRYSEDRIGLADYALESGGASVISTRCSETYETKTALLSLFGIPLWYHSQSPRVILQPDVHPGNCWAFQGPQGFAVVRLSARIRPTAVTLEHVPKALSPNSTISSAPKDFAIFGFDEDLQQEGTLLGKFTYDQDGEPIQTFHFQAPTMATYQVVELRILTNWGHPEYTCIYRFRVHGEPAH  717
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.........hhhhh.eeee...........eeeee..eeeeee..hhhhhhh........eeee...eeeeeeeeeeeeeeeeeee..hhhhhhhhh......eeeeeee........eeeeeee.......eeeee........eeeeeeee........eeee.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------S---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------SUN  PDB: A:555-716 UniProt: 555-716                                                                                                                              - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4dxs A  522 GVTEEQVHHIVKQALQRYSEDRIGLADYALESGGASVISTRCSETYETKTALLSLFGIPLWYHSQSPRVILQPDVHPGNCWAFQGPQGFAVVRLSARIRPTAVTLEHVPKALSPNSTISSAPKDFAIFGFDEDLQQEGTLLGKFTYDQDGEPIQTFHFQAPTMATYQVVELRILTNWGHPEYTCIYRFRVHGEPAH  717
                                   531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711

Chain B from PDB  Type:PROTEIN  Length:24
 aligned with SYNE2_HUMAN | Q8WXH0 from UniProtKB/Swiss-Prot  Length:6885

    Alignment length:24
                                  6871      6881    
         SYNE2_HUMAN   6862 CTQANNFARSFYPMLRYTNGPPPT 6885
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author .....hhhhh...eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
                 Transcript ------------------------ Transcript
                4dxs B 6862 CTQANNFARSFYPMLRYTNGPPPT 6885
                                  6871      6881

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 4DXS)

(no "CATH Domain" information available for 4DXS)

(no "Pfam Domain" information available for 4DXS)

Asymmetric Unit(hide GO term definitions)

Chain A (SUN2_HUMAN | Q9UH99)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005521	lamin binding	Interacting selectively and non-covalently with lamin; any of a group of intermediate-filament proteins that form the fibrous matrix on the inner surface of the nuclear envelope.
	GO:0008017	microtubule binding	Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
	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).
biological process
	GO:0051642	centrosome localization	Any process in which a centrosome is transported to, and/or maintained in, a specific location within the cell.
	GO:0090286	cytoskeletal anchoring at nuclear membrane	The process in which cytoskeletal filaments are directly or indirectly linked to the nuclear membrane.
	GO:0007052	mitotic spindle organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.
	GO:0006998	nuclear envelope organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope.
	GO:0090292	nuclear matrix anchoring at nuclear membrane	The process in which the nuclear matrix, the dense fibrillar network lying on the inner side of the nuclear membrane, is directly or indirectly linked to the nuclear membrane.
	GO:0007097	nuclear migration	The directed movement of the nucleus.
	GO:0031022	nuclear migration along microfilament	The directed movement of the nucleus along microfilaments within the cell, mediated by motor proteins.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
cellular component
	GO:0034993	LINC complex	A protein complex that spans the nuclear outer and inner membranes, thereby linking the major cytoplasmic cytoskeleton elements to the nuclear lumen; the complex is conserved in eukaryotes and contains proteins with SUN and KASH domains.
	GO:0000794	condensed nuclear chromosome	A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005639	integral component of nuclear inner membrane	The component of the nuclear inner membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0005635	nuclear envelope	The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
	GO:0005637	nuclear inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope.
	GO:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	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.

Chain B (SYNE2_HUMAN | Q8WXH0)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0051015	actin filament binding	Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
	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).
biological process
	GO:0051642	centrosome localization	Any process in which a centrosome is transported to, and/or maintained in, a specific location within the cell.
	GO:0090286	cytoskeletal anchoring at nuclear membrane	The process in which cytoskeletal filaments are directly or indirectly linked to the nuclear membrane.
	GO:0007163	establishment or maintenance of cell polarity	Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns.
	GO:0010761	fibroblast migration	Cell migration that is accomplished by extension and retraction of a fibroblast pseudopodium. A fibroblast is a connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules.
	GO:0006998	nuclear envelope organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope.
	GO:0007097	nuclear migration	The directed movement of the nucleus.
	GO:0031022	nuclear migration along microfilament	The directed movement of the nucleus along microfilaments within the cell, mediated by motor proteins.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0034504	protein localization to nucleus	A process in which a protein transports or maintains the localization of another protein to the nucleus.
cellular component
	GO:0034993	LINC complex	A protein complex that spans the nuclear outer and inner membranes, thereby linking the major cytoplasmic cytoskeleton elements to the nuclear lumen; the complex is conserved in eukaryotes and contains proteins with SUN and KASH domains.
	GO:0030018	Z disc	Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
	GO:0016235	aggresome	An inclusion body formed by dynein-dependent retrograde transport of an aggregated protein on microtubules.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	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: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:0031527	filopodium membrane	The portion of the plasma membrane surrounding a filopodium.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0045111	intermediate filament cytoskeleton	Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell.
	GO:0031258	lamellipodium membrane	The portion of the plasma membrane surrounding a lamellipodium.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0030016	myofibril	The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism.
	GO:0005635	nuclear envelope	The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
	GO:0031981	nuclear lumen	The volume enclosed by the nuclear inner membrane.
	GO:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	GO:0005640	nuclear outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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:0016529	sarcoplasmic reticulum	A fine reticular network of membrane-limited elements that pervades the sarcoplasm of a muscle cell; continuous over large portions of the cell and with the nuclear envelope; that part of the endoplasmic reticulum specialized for calcium release, uptake and storage.
	GO:0033017	sarcoplasmic reticulum membrane	The lipid bilayer surrounding the sarcoplasmic reticulum.

Asymmetric Unit
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	4dxs
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	SUN2_HUMAN \| Q9UH99	:	3unp 4dxr 4dxt 4fi9
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