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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CD14

Authors :   J. -I. Kim, C. J. Lee, M. S. Jin, C. -H. Lee, S. -G. Paik, H. Lee, J. -O. Lee

Date :   06 Jan 05 (Deposition) - 22 Feb 05 (Release) - 10 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Cd14, Lps, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. -I. Kim, C. J. Lee, M. S. Jin, C. -H. Lee, S. -G. Paik, H. Lee, J. -O. Lee
Crystal Structure Of Cd14 And Its Implications For Lipopolysaccharide Signaling
J. Biol. Chem. V. 280 11347 2005
PubMed-ID: 15644310 | Reference-DOI: 10.1074/JBC.M414607200

Molecule 1 - MONOCYTE DIFFERENTIATION ANTIGEN CD14
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	RESIDUES 3-314
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	MYELOID CELL-SPECIFIC LEUCINE-RICH GLYCOPROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 10)

No.	Name	Count	Type	Full Name
1	NAG	10	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 10)

No.	Name	Count	Type	Full Name
1	NAG	10	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 3 (1, 5)

No.	Name	Count	Type	Full Name
1	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:238 , HIS A:239 , ASN A:261 , SER A:263 , ASP A:282 , NAG A:1412 , HOH A:1462 , HOH A:1495	BINDING SITE FOR RESIDUE NAG A 1411
02	AC2	SOFTWARE	LEU A:117 , NAG A:1411	BINDING SITE FOR RESIDUE NAG A 1412
03	AC3	SOFTWARE	ASN A:106 , GLU A:108 , ASN A:132 , NAG A:1414	BINDING SITE FOR RESIDUE NAG A 1413
04	AC4	SOFTWARE	NAG A:1413 , HOH A:1521	BINDING SITE FOR RESIDUE NAG A 1414
05	AC5	SOFTWARE	ASN A:165 , HOH A:1512	BINDING SITE FOR RESIDUE NAG A 1415
06	AC6	SOFTWARE	SER B:238 , HIS B:239 , ASN B:261 , SER B:263 , ASP B:282 , NAG B:1412 , HOH B:1537 , HOH B:1590	BINDING SITE FOR RESIDUE NAG B 1411
07	AC7	SOFTWARE	PHE B:264 , NAG B:1411 , HOH B:1439	BINDING SITE FOR RESIDUE NAG B 1412
08	AC8	SOFTWARE	ASN B:106 , LEU B:107 , GLU B:108 , ASN B:132 , PRO B:175 , NAG B:1414 , HOH B:1494 , HOH B:1584	BINDING SITE FOR RESIDUE NAG B 1413
09	AC9	SOFTWARE	GLY B:43 , NAG B:1413	BINDING SITE FOR RESIDUE NAG B 1414
10	BC1	SOFTWARE	ASN B:165 , SER B:195	BINDING SITE FOR RESIDUE NAG B 1415

Asymmetric Unit

No.	Residues
1	A:8	-	A:17
2	A:15	-	A:32
3	A:17	-	A:32
4	A:168	-	A:198
5	A:222	-	A:251
6	B:8	-	B:17
7	B:15	-	B:32
8	B:168	-	B:198
9	B:222	-	B:251

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

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

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	CD14_MOUSE	191-213 246-267 292-313	6	A:176-198 B:176-198 A:231-252 B:231-252 A:277-298 B:277-298

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	CD14_MOUSE	191-213 246-267 292-313	6	A:176-198 B:176-198 A:231-252 B:231-252 A:277-298 B:277-298

Biological Unit 2 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	CD14_MOUSE	191-213 246-267 292-313	3	A:176-198 - A:231-252 - A:277-298 -

Biological Unit 3 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	CD14_MOUSE	191-213 246-267 292-313	3	- B:176-198 - B:231-252 - B:277-298

(no "Exon" information available for 1WWL)

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:308
 aligned with CD14_MOUSE | P10810 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:308
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321        
           CD14_MOUSE    22 PCELDEESCSCNFSDPKPDWSSAFNCLGAADVELYGGGRSLEYLLKRVDTEADLGQFTDIIKSLSLKRLTVRAARIPSRILFGALRVLGISGLQELTLENLEVTGTAPPPLLEATGPDLNILNLRNVSWATRDAWLAELQQWLKPGLKVLSIAQAHSLNFSCEQVRVFPALSTLDLSDNPELGERGLISALCPLKFPTLQVLALRNAGMETPSGVCSALAAARVQLQGLDLSHNSLRDAAGAPSCDWPSQLNSLNLSFTGLKQVPKGLPAKLSVLDLSYNRLDRNPSPDELPQVGNLSLKGNPFLDSE 329
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1wwlA00 A:7-314 Ribonuclease Inhibitor                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..ee.........hhhhhhhh....eeeeeeeeee..hhhhhh.....hhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhh.....eeeeeee...................eeeee........hhhhhhhh.......eeeee...................eee......hhhhhhhhhh.........eee.......hhhhhhhhhhhh.....eee......................eee...............eeeeee................eeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR  PDB: A:176-198    --------------------------------LRR  PDB: A:231-252   ------------------------LRR  PDB: A:277-298   ---------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wwl A   7 PCELDEESCSCNFSDPKPDWSSAFNCLGAADVELYGGGRSLEYLLKRVDTEADLGQFTDIIKSLSLKRLTVRAARIPSRILFGALRVLGISGLQELTLENLEVTGTAPPPLLEATGPDLNILNLRNVSWATRDAWLAELQQWLKPGLKVLSIAQAHSLNFSCEQVRVFPALSTLDLSDNPELGERGLISALCPLKFPTLQVLALRNAGMETPSGVCSALAAARVQLQGLDLSHNSLRDAAGAPSCDWPSQLNSLNLSFTGLKQVPKGLPAKLSVLDLSYNRLDRNPSPDELPQVGNLSLKGNPFLDSE 314
                                    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

Chain B from PDB  Type:PROTEIN  Length:312
 aligned with CD14_MOUSE | P10810 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:312
                                    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  
           CD14_MOUSE    18 APPEPCELDEESCSCNFSDPKPDWSSAFNCLGAADVELYGGGRSLEYLLKRVDTEADLGQFTDIIKSLSLKRLTVRAARIPSRILFGALRVLGISGLQELTLENLEVTGTAPPPLLEATGPDLNILNLRNVSWATRDAWLAELQQWLKPGLKVLSIAQAHSLNFSCEQVRVFPALSTLDLSDNPELGERGLISALCPLKFPTLQVLALRNAGMETPSGVCSALAAARVQLQGLDLSHNSLRDAAGAPSCDWPSQLNSLNLSFTGLKQVPKGLPAKLSVLDLSYNRLDRNPSPDELPQVGNLSLKGNPFLDSE 329
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1wwlB00 B:3-314 Ribonuclease Inhibitor                                                                                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR_6-1wwlB01 B:174-199   ------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR_6-1wwlB02 B:174-199   ------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....ee....eeeee..................eeeee.......hhhhhh........hhhhhhhh...eeeeeee..hhhhhhhhhhhhh.....eeeeeeee..................eeeeeeee.....hhhhhhhhh......eeeee...................eee......hhhhhhhh...........eee.......hhhhhhhhhhhhh....eee......................eee...............eeeeee................eeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR  PDB: B:176-198    --------------------------------LRR  PDB: B:231-252   ------------------------LRR  PDB: B:277-298   ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wwl B   3 ADPEPCELDEESCSCNFSDPKPDWSSAFNCLGAADVELYGGGRSLEYLLKRVDTEADLGQFTDIIKSLSLKRLTVRAARIPSRILFGALRVLGISGLQELTLENLEVTGTAPPPLLEATGPDLNILNLRNVSWATRDAWLAELQQWLKPGLKVLSIAQAHSLNFSCEQVRVFPALSTLDLSDNPELGERGLISALCPLKFPTLQVLALRNAGMETPSGVCSALAAARVQLQGLDLSHNSLRDAAGAPSCDWPSQLNSLNLSFTGLKQVPKGLPAKLSVLDLSYNRLDRNPSPDELPQVGNLSLKGNPFLDSE 314
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312

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 1WWL)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Horseshoe (92)

Topology: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) (73)

Homologous Superfamily: Ribonuclease Inhibitor (73)

House mouse (Mus musculus) (1)

1a	1wwlA00	A:7-314
1b	1wwlB00	B:3-314

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: LRR (77)

Family: LRR_6 (24)

Mus musculus (Mouse) (3)

1a	LRR_6-1wwlB01	B:174-199
1b	LRR_6-1wwlB02	B:174-199

Asymmetric Unit(hide GO term definitions)

Chain A,B (CD14_MOUSE | P10810)

molecular function
	GO:0001530	lipopolysaccharide binding	Interacting selectively and non-covalently with lipopolysaccharide.
	GO:0070891	lipoteichoic acid binding	Interacting selectively and non-covalently with lipoteichoic acid.
biological process
	GO:0071726	cellular response to diacyl bacterial lipopeptide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a diacylated bacterial lipopeptide stimulus.
	GO:0071222	cellular response to lipopolysaccharide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0071223	cellular response to lipoteichoic acid	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipoteichoic acid stimulus; lipoteichoic acid is a major component of the cell wall of gram-positive bacteria and typically consists of a chain of glycerol-phosphate repeating units linked to a glycolipid anchor.
	GO:0071727	cellular response to triacyl bacterial lipopeptide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a triacylated bacterial lipopeptide stimulus.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0031663	lipopolysaccharide-mediated signaling pathway	A series of molecular signals initiated by the binding of a lipopolysaccharide (LPS) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Lipopolysaccharides are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system.
	GO:0050715	positive regulation of cytokine secretion	Any process that activates or increases the frequency, rate or extent of the regulated release of cytokines from a cell.
	GO:0045807	positive regulation of endocytosis	Any process that activates or increases the frequency, rate or extent of endocytosis.
	GO:0032729	positive regulation of interferon-gamma production	Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
	GO:0032760	positive regulation of tumor necrosis factor production	Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.
	GO:0032481	positive regulation of type I interferon production	Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	GO:0006898	receptor-mediated endocytosis	An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
	GO:0009617	response to bacterium	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
	GO:0051602	response to electrical stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electrical stimulus.
	GO:0045471	response to ethanol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
	GO:0009408	response to heat	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0032026	response to magnesium ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a magnesium ion stimulus.
	GO:0002237	response to molecule of bacterial origin	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin.
	GO:0034612	response to tumor necrosis factor	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
	GO:0034142	toll-like receptor 4 signaling pathway	Any series of molecular signals generated as a consequence of binding to toll-like receptor 4.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0031362	anchored component of external side of plasma membrane	The component of the plasma membrane consisting of the gene products that are tethered to the external side of the membrane only by a covalently attached anchor, such as a lipid group embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0031225	anchored component of membrane	The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0046696	lipopolysaccharide receptor complex	A multiprotein complex that consists of at least three proteins, CD14, TLR4, and MD-2, each of which is glycosylated and which functions as a lipopolysaccharide (LPS) receptor that primes the innate immune response against bacterial pathogens.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	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.

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	Cis Peptide Bonds
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Description

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Ligands, Modified Residues, Ions (1, 10)

Sites (10, 10)

SS Bonds (9, 9)

Cis Peptide Bonds (0, 0)

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