1JHN - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE LUMENAL DOMAIN OF CALNEXIN

Authors :   J. D. Schrag, J. M. Bergeron, Y. Li, S. Borisova, M. Hahn, D. Y. Thomas, M. Cygler

Date :   28 Jun 01 (Deposition) - 10 Oct 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A

Keywords :   Jelly-Roll, Beta Sandwich, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. D. Schrag, J. J. Bergeron, Y. Li, S. Borisova, M. Hahn, D. Y. Thomas, M. Cygler
The Structure Of Calnexin, An Er Chaperone Involved In Quality Control Of Protein Folding.
Mol. Cell V. 8 633 2001
PubMed-ID: 11583625 | Reference-DOI: 10.1016/S1097-2765(01)00318-5
(for further references see the PDB file header)

Molecule 1 - CALNEXIN
	Cell Line	:	SF9
	Chains	:	A
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Expression System Vector	:	PBLUBAC
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	LUMENAL DOMAIN (RESIDUES 45-468)
	Organism Common	:	DOG
	Organism Scientific	:	CANIS LUPUS FAMILIARIS
	Organism Taxid	:	9615
	Strain	:	FAMILIARIS

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:75 , ASP A:118 , LYS A:119 , ASP A:437	BINDING SITE FOR RESIDUE CA A 900

Asymmetric/Biological Unit

No.	Residues
1	A:161	-	A:195
2	A:361	-	A:367

(no "Cis Peptide Bond" information available for 1JHN)

(no "SAP(SNP)/Variant" information available for 1JHN)

Asymmetric/Biological Unit (3, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CALRETICULIN_1	PS00803	Calreticulin family signature 1.	CALX_CANLF	154-169	1	A:154-169
2	CALRETICULIN_2	PS00804	Calreticulin family signature 2.	CALX_CANLF	188-196	1	A:188-196
3	CALRETICULIN_REPEAT	PS00805	Calreticulin family repeated motif signature.	CALX_CANLF	277-289 294-306 332-344	3	A:277-289 A:294-306 A:332-344

(no "Exon" information available for 1JHN)

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:380
 aligned with CALX_CANLF | P24643 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:398
                                    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       450        
           CALX_CANLF    61 YKAPVPTGEVYFADSFDRGTLSGWILSKAKKDDTDDEIAKYDGKWEVDEMKETKLPGDKGLVLMSRAKHHAISAKLNKPFLFDTKPLIVQYEVNFQNGIECGGAYVKLLSKTPELNLDQFHDKTPYTIMFGPDKCGEDYKLHFIFRHKNPKTGVYEEKHAKRPDADLKTYFTDKKTHLYTLILNPDNSFEILVDQSIVNSGNLLNDMTPPVNPSREIEDPEDQKPEDWDERPKIPDPDAVKPDDWNEDAPAKIPDEEATKPDGWLDDEPEYVPDPDAEKPEDWDEDMDGEWEAPQIANPKCESAPGCGVWQRPMIDNPNYKGKWKPPMIDNPNYQGIWKPRKIPNPDFFEDLEPFKMTPFSAIGLELWSMTSDIFFDNFIVCGDRRVVDDWANDGWGL 458
               SCOP domains d1jhna4 A:61-262,A:412-458 Cal           nexin                                                                                                                                                                   d1jhna3 A:270-411 Calnexin                                                                                                                    d1jhna4 A:61-262,A:412-458 Calnexin             SCOP domains
               CATH domains 1jhnA01 A:61-262,A:416-456  [c           ode=2.60.120.200, no name defined]                                                                                                                                      1jhnA02 A:270-415 Calnexin lumenal domain, non-globular proline-rich hairpin domain                                                               1jhnA01 A:61-262,A:416-456               -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee................-----------.............................eeeeeeeeee......eeeeeee.......eee..eeee......hhhhh.....eeeeeeeeee...................................................................-------..........................................eee...........................................................eee...........eee.............................eeeeee...........eeeeee................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------CALRETICULIN_1  ------------------CALRETICU--------------------------------------------------------------------------------CALRETICULIN_----CALRETICULIN_-------------------------CALRETICULIN_------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jhn A  61 YKAPVPSGEVYFADSFDRGTLSGWILSKAK-----------DGKWEVDEMKETKLPGDKGLVLMSRAKHHAISAKLNKPFLFDTKPLIVQYEVNFQNGIECGGAYVKLLSKTPELNLDQFHDKTPYTIMFGPDKCGEDYKLHFIFRHKNPKTGVYEEKHAKRPDADLKTYFTDKKTHLYTLILNPDNSFEILVDQSIVNSGN-------PVNPSREIEDPEDQKPEDWDERPKIPDPDAVKPDDWNEDAPAKIPDEEATKPDGWLDDEPEYVPDPDAEKPEDWDEDMDGEWEAPQIANPKCESAPGCGVWQRPMIDNPNYKGKWKPPMIDNPNYQGIWKPRKIPNPDFFEDLEPFKMTPFSAIGLELWSMTSDIFFDNFIVCGDRRVVDDWANDGWGL 458
                                    70        80        90         - |     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       450        
                                                        90         102                                                                                                                                                             262     270

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: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Calnexin lumenal domain, non-globular proline-rich hairpin domain (3)

Homologous Superfamily: Calnexin lumenal domain, non-globular proline-rich hairpin domain (3)

Dog (Canis lupus familiaris) (1)

1jhnA02

A:270-415

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.200, no name defined] (421)

Dog (Canis lupus familiaris) (1)

1jhnA01

A:61-262,A:416-456

(no "Pfam Domain" information available for 1JHN)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CALX_CANLF | P24643)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0051082	unfolded protein binding	Interacting selectively and non-covalently with an unfolded protein.
biological process
	GO:0072583	clathrin-dependent endocytosis	An endocytosis process that begins when material is taken up into clathrin-coated pits, which then pinch off to form clathrin-coated endocytic vesicles.
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	GO:0048488	synaptic vesicle endocytosis	Clathrin-mediated endocytosis of presynaptic membrane that recycles synaptic vesicle membrane and its components following synaptic vesicle exocytosis. This process starts with coating of the membrane with adaptor proteins and clathrin prior to invagination and ends when uncoating has finished.
cellular component
	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:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	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:0042470	melanosome	A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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	1jhn
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 5)

Exons (0, 0)

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