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Title :   CRYSTAL STRUCTURE OF MOUSE RANK

Authors :   S. W. Walter, C. Liu, X. Zhu, Y. Wu, R. J. Owens, D. I. Stuart, B. Gao, J. Ren

Date :   31 Mar 10 (Deposition) - 02 Jun 10 (Release) - 02 Jun 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.01

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

Keywords :   Rank, Rankl, Rankl-Rank Complex, Tnfsf11, Tnfrsf11A, Tnf Superfamily, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Liu, T. S. Walter, P. Huang, S. Zhang, X. Zhu, Y. Wu, L. R. Wedderburn, P. Tang, R. J. Owens, D. I. Stuart, J. Ren, B. Gao
Structural And Functional Insights Of Rankl-Rank Interaction And Signaling.
J. Immunol. 2010
PubMed-ID: 20483727 | Reference-DOI: 10.4049/JIMMUNOL.0904033

Molecule 1 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 11A
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21-GOLD(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 26-210
	Gene	:	TNFRSF11A
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	RAW264.7
	Synonym	:	RECEPTOR ACTIVATOR OF NF-KB, OSTEOCLAST DIFFERENTIATION FACTOR RECEPTOR, ODFR, RANK

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 13)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CL	3	Ligand/Ion	CHLORIDE ION
3	GOL	4	Ligand/Ion	GLYCEROL
4	NA	2	Ligand/Ion	SODIUM ION
5	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:134 , ALA A:135 , PHE A:138 , SER A:161 , VAL A:163 , HOH A:320	BINDING SITE FOR RESIDUE NA A 1
02	AC2	SOFTWARE	TYR A:77 , HIS A:90 , ARG A:111 , HOH A:268	BINDING SITE FOR RESIDUE CL A 219
03	AC3	SOFTWARE	THR A:188 , THR A:189 , ARG B:130	BINDING SITE FOR RESIDUE SO4 A 220
04	AC4	SOFTWARE	HIS A:185 , GLN A:186 , ARG B:129	BINDING SITE FOR RESIDUE SO4 A 221
05	AC5	SOFTWARE	TRP A:173 , THR A:174 , ASN A:175 , CYS A:176 , THR A:177 , GLU A:183	BINDING SITE FOR RESIDUE GOL A 222
06	AC6	SOFTWARE	VAL A:102 , ASP A:103 , ASN A:106 , ALA A:109 , PRO A:110 , ARG A:111 , ARG A:112 , HOH A:351	BINDING SITE FOR RESIDUE GOL A 223
07	AC7	SOFTWARE	PRO A:74 , TYR A:119 , CYS A:128 , HOH A:235 , HOH A:237 , HOH A:264 , HOH A:370	BINDING SITE FOR RESIDUE GOL A 224
08	AC8	SOFTWARE	GLN A:141 , PRO A:143 , GLN A:145 , HOH A:254 , HOH A:299 , HOH A:341 , TRP B:121	BINDING SITE FOR RESIDUE GOL A 225
09	AC9	SOFTWARE	GLU A:76 , CYS A:87	BINDING SITE FOR RESIDUE ACT A 226
10	BC1	SOFTWARE	PHE A:159 , HOH A:258 , HOH A:259	BINDING SITE FOR RESIDUE ACT A 227
11	BC2	SOFTWARE	CYS B:134 , ALA B:135 , PHE B:138 , SER B:161 , VAL B:163 , HOH B:251	BINDING SITE FOR RESIDUE NA B 2
12	BC3	SOFTWARE	CYS B:134 , ALA B:135	BINDING SITE FOR RESIDUE CL B 219
13	BC4	SOFTWARE	HIS B:90 , LYS B:91 , HOH B:229	BINDING SITE FOR RESIDUE CL B 220

Asymmetric/Biological Unit

No.	Residues
1	A:35	-	A:47
2	A:48	-	A:61
3	A:51	-	A:69
4	A:72	-	A:87
5	A:93	-	A:113
6	A:115	-	A:128
7	A:125	-	A:127
8	A:134	-	A:152
9	A:155	-	A:170
10	A:176	-	A:195
11	B:48	-	B:61
12	B:51	-	B:69
13	B:72	-	B:87
14	B:93	-	B:113
15	B:115	-	B:128
16	B:125	-	B:127
17	B:134	-	B:152
18	B:155	-	B:170

Asymmetric/Biological Unit

No.	Residues
1	Pro A:33	-	Pro A:34
2	His A:142	-	Pro A:143
3	His B:142	-	Pro B:143

(no "SAP(SNP)/Variant" information available for 3ME4)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TNFR_NGFR_2	PS50050	TNFR/NGFR family cysteine-rich region domain profile.	TNR11_MOUSE	34-69	1	A:34-69
2	TNFR_NGFR_1	PS00652	TNFR/NGFR family cysteine-rich region signature.	TNR11_MOUSE	35-69	1	A:35-69

(no "Exon" information available for 3ME4)

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:169
 aligned with TNR11_MOUSE | O35305 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:169
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192         
          TNR11_MOUSE    33 PPCTQERHYEHLGRCCSRCEPGKYLSSKCTPTSDSVCLPCGPDEYLDTWNEEDKCLLHKVCDAGKALVAVDPGNHTAPRRCACTAGYHWNSDCECCRRNTECAPGFGAQHPLQLNKDTVCTPCLLGFFSDVFSSTDKCKPWTNCTLLGKLEAHQGTTESDVVCSSSMTL 201
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee..eeee.....eeeee........eeee....ee..........ee....hhhh.eeee.........eeee...eeee....eeee.......eee...ee......eee....ee..........ee..hhhhhh..eee........ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -TNFR_NGFR_2  PDB: A:34-69           ------------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) --TNFR_NGFR_1  PDB: A:35-69          ------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3me4 A  33 PPCTQERHYEHLGRCCSRCEPGKYLSSKCTPTSDSVCLPCGPDEYLDTWNEEDKCLLHKVCDAGKALVAVDPGNHTAPRRCACTAGYHWNSDCECCRRNTECAPGFGAQHPLQLNKDTVCTPCLLGFFSDVFSSTDKCKPWTNCTLLGKLEAHQGTTESDVVCSSSMTL 201
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192

Chain B from PDB  Type:PROTEIN  Length:150
 aligned with TNR11_MOUSE | O35305 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:159
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185         
          TNR11_MOUSE    36 TQERHYEHLGRCCSRCEPGKYLSSKCTPTSDSVCLPCGPDEYLDTWNEEDKCLLHKVCDAGKALVAVDPGNHTAPRRCACTAGYHWNSDCECCRRNTECAPGFGAQHPLQLNKDTVCTPCLLGFFSDVFSSTDKCKPWTNCTLLGKLEAHQGTTESDVV 194
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) TNFR_c6-3me4B01 B:36-69           ----------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) TNFR_c6-3me4B02 B:36-69           ----------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eeee..eeee.....eeeee........eeee....ee..........ee....hhhh.eee..........eeee...eeee....eeee.......eee...ee......eee....ee..........ee....---------......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TNFR_NGFR_2  PDB: - UniProt: 34-69----------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) TNFR_NGFR_1  PDB: - UniProt: 35-69----------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3me4 B  36 TQERHYEHLGRCCSRCEPGKYLSSKCTPTSDSVCLPCGPDEYLDTWNEEDKCLLHKVCDAGKALVAVDPGNHTAPRRCACTAGYHWNSDCECCRRNTECAPGFGAQHPLQLNKDTVCTPCLLGFFSDVFSSTDKCKPWTNC---------QGTTESDVV 194
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175|        -|        
                                                                                                                                                                      176       186

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 3ME4)

(no "CATH Domain" information available for 3ME4)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: TNFR_c6] (13)

Family: TNFR_c6 (13)

Mus musculus (Mouse) (3)

1a	TNFR_c6-3me4B01	B:36-69
1b	TNFR_c6-3me4B02	B:36-69

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TNR11_MOUSE | O35305)

molecular function
	GO:0019955	cytokine binding	Interacting selectively and non-covalently with a cytokine, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0004888	transmembrane signaling receptor activity	Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
	GO:0005031	tumor necrosis factor-activated receptor activity	Combining with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages, to initiate a change in cell function.
biological process
	GO:0071847	TNFSF11-mediated signaling pathway	A series of molecular signals initiated by the binding of tumor necrosis factor ligand superfamily member 11 (TNFSF11) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0002250	adaptive immune response	An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
	GO:0097190	apoptotic signaling pathway	A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
	GO:0060086	circadian temperature homeostasis	Any homeostatic process in which an organism modulates its internal body temperature at different values with a regularity of approximately 24 hours.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0048535	lymph node development	The process whose specific outcome is the progression of lymph nodes over time, from their formation to the mature structure. A lymph node is a round, oval, or bean shaped structure localized in clusters along the lymphatic vessels, with a distinct internal structure including specialized vasculature and B- and T-zones for the activation of lymphocytes.
	GO:0060749	mammary gland alveolus development	The progression of the mammary gland alveolus over time, from its formation to its mature state. The mammary gland alveolus is a sac-like structure that is found in the mature gland.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0001503	ossification	The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
	GO:0030316	osteoclast differentiation	The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue.
	GO:0071848	positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling	Any TNFSF11-mediated signaling process that increases the rate, frequency, or extent of the ERK1 and ERK2 cascade.
	GO:0043507	positive regulation of JUN kinase activity	Any process that activates or increases the frequency, rate or extent of JUN kinase activity.
	GO:0043410	positive regulation of MAPK cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
	GO:0051092	positive regulation of NF-kappaB transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
	GO:0071812	positive regulation of fever generation by positive regulation of prostaglandin secretion	Any process that increases the rate or extent of fever generation via positive regulation of the frequency, rate or extent of the regulated release of a prostaglandin from a cell.
	GO:0051091	positive regulation of sequence-specific DNA binding transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0034097	response to cytokine	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 cytokine stimulus.
	GO:0070555	response to interleukin-1	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 interleukin-1 stimulus.
	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:0009314	response to radiation	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 electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
	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:0033209	tumor necrosis factor-mediated signaling pathway	A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	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: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:0005887	integral component of plasma membrane	The component of the plasma 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: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.

Asymmetric/Biological Unit
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		Pro A:33 - Pro A:34	[ RasMol ]

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	TNR11_MOUSE \| O35305	:	3me2 3qbq 4giq 5bnq

3me2	CRYSTAL STRUCTURE OF MOUSE RANKL-RANK COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 13)

Sites (13, 13)

SS Bonds (18, 18)

Cis Peptide Bonds (3, 3)

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SAPs(SNPs)/Variants (0, 0)

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