3D48 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF A PROLACTIN RECEPTOR ANTAGONIST BOUND TO THE EXTRACELLULAR DOMAIN OF THE PROLACTIN RECEPTOR

Authors :   L. A. Svensson, J. Breinholt

Date :   14 May 08 (Deposition) - 03 Jun 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : P,R

Keywords :   Cytokine-Cytokine Receptor Complex, Four-Helix Bundle, Glycoprotein, Hormone, Lactation, Secreted, Alternative Splicing, Membrane, Receptor, Transmembrane, Hormone/Hormone Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. A. Svensson, K. Bondensgaard, L. Norskov-Lauritsen, L. Christensen, P. Becker, M. D. Andersen, M. J. Maltesen, K. D. Rand, J. Breinholt
Crystal Structure Of A Prolactin Receptor Antagonist Bound To The Extracellular Domain Of The Prolactin Receptor
J. Biol. Chem. V. 283 19085 2008
PubMed-ID: 18467331 | Reference-DOI: 10.1074/JBC.M801202200
(for further references see the PDB file header)

Molecule 1 - PROLACTIN
	Chains	:	P
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32-A(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 12-199
	Gene	:	PRL
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PRL

Molecule 2 - PROLACTIN RECEPTOR
	Chains	:	R
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET39-B(+)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	EXTRACELLULAR DOMAIN
	Gene	:	PRLR
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PRL-R

		1	2
Asymmetric/Biological Unit	:	P	R

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CO3	4	Ligand/Ion	CARBONATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER P:57 , CYS P:58 , HIS P:59 , LEU P:171 , CYS P:174	BINDING SITE FOR RESIDUE CO3 P 1
2	AC2	SOFTWARE	TYR R:190 , TRP R:191	BINDING SITE FOR RESIDUE CO3 R 211
3	AC3	SOFTWARE	CYS R:12 , ARG R:13 , GLN R:102	BINDING SITE FOR RESIDUE CO3 R 212
4	AC4	SOFTWARE	THR R:39 , TYR R:40 , HIS R:41 , ILE R:76 , MET R:78	BINDING SITE FOR RESIDUE CO3 R 213

Asymmetric/Biological Unit

No.	Residues
1	P:58	-	P:174
2	R:12	-	R:22
3	R:51	-	R:62

(no "Cis Peptide Bond" information available for 3D48)

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049172	I	100	V	PRLR_HUMAN	Polymorphism	2228482	R	I	76	V
2	UniProt	VAR_070894	I	170	L	PRLR_HUMAN	Disease (MFAB)	72478580	R	I	146	L
3	UniProt	VAR_070895	H	212	R	PRLR_HUMAN	Disease (HPRL)	398122522	R	H	188	R

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

Asymmetric/Biological Unit (4, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FN3	PS50853	Fibronectin type-III domain profile.	PRLR_HUMAN	27-128 129-229	2	R:3-104 R:105-204
2	SOMATOTROPIN_1	PS00266	Somatotropin, prolactin and related hormones signature 1.	PRL_HUMAN	86-119	1	P:58-91
3	HEMATOPO_REC_L_F1	PS01352	Long hematopoietin receptor, single chain family signature.	PRLR_HUMAN	147-224	1	R:123-200
4	SOMATOTROPIN_2	PS00338	Somatotropin, prolactin and related hormones signature 2.	PRL_HUMAN	202-219	1	P:174-191

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000306482	1	ENSE00001148399	chr6:22297730-22297184	547	PRL_HUMAN	1-10	10	0	-	-
1.2c	ENST00000306482	2c	ENSE00001174381	chr6:22294813-22294638	176	PRL_HUMAN	10-68	59	1	P:13-40	28
1.3	ENST00000306482	3	ENSE00001174368	chr6:22292874-22292767	108	PRL_HUMAN	69-104	36	1	P:41-76 (gaps)	36
1.4	ENST00000306482	4	ENSE00001174359	chr6:22290582-22290403	180	PRL_HUMAN	105-164	60	1	P:77-136 (gaps)	60
1.5	ENST00000306482	5	ENSE00001148390	chr6:22287822-22287480	343	PRL_HUMAN	165-227	63	1	P:137-198 (gaps)	62

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 P from PDB  Type:PROTEIN  Length:165
 aligned with PRL_HUMAN | P01236 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:186
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
            PRL_HUMAN    41 VTLRDLFDRAVVLSHYIHNLSSEMFSEFDKRYTHGRGFITKAINSCHTSSLATPEDKEQAQQMNQKDFLSLIVSILRSWNEPLYHLVTEVRGMQEAPEAILSKAVEIEEQTKRLLEGMELIVSQVHPETKENEIYPVWSGLPSLQMADEESRLSAYYNLLHCLRRDSHKIDNYLKLLKCRIIHNNN 226
               SCOP domains d3d48p_ P: Prolactin (placenta      l lactogen)                                                                                                                                            SCOP domains
               CATH domains 3d48P00 P:13-198  [code=1.20.1      250.10, no name defined]                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh.------.hhhhhh..hhhhhh....hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh-------hhhhhhhhhhhhhhhhhhhhhhhhhhh--------......hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ---------------------------------------------SOMATOTROPIN_1  PDB: P:58-91      ----------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------SOMATOTROPIN_2    ------- PROSITE (3)
               Transcript 1 Exon 1.2c  PDB: P:13-40     Exon 1.3  PDB: P:41-76 (gaps)       Exon 1.4  PDB: P:77-136 (gaps) UniProt: 105-164             Exon 1.5  PDB: P:137-198 (gaps) UniProt: 165-227 [INCOMPLETE]  Transcript 1
                 3d48 P  13 VTLRDLFDRAVVLSHYIHNLSSEMFSEFDK------GFITKAINSCHTSSLATPEDKEQAQQMNQKDFLSLIVSILRSWNEPLYHLVTEVR-------AILSKAVEIEEQTKRLLERMELIVSQV--------IYPVWSGLPSLQMADEESRLSAYYNLLHCLRRDSHKIDNYLKLLKCRIIHNNN 198
                                    22        32        42      | 52        62        72        82        92       102|      112       122       132    |    -   |   152       162       172       182       192      
                                                        42     49                                                   103     111                       137      146

Chain R from PDB  Type:PROTEIN  Length:195
 aligned with PRLR_HUMAN | P16471 from UniProtKB/Swiss-Prot  Length:622

    Alignment length:203
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225   
           PRLR_HUMAN    26 LPPGKPEIFKCRSPNKETFTCWWRPGTDGGLPTNYSLTYHREGETLMHECPDYITGGPNSCHFGKQYTSMWRTYIMMVNATNQMGSSFSDELYVDVTYIVQPDPPLELAVEVKQPEDRKPYLWIKWSPPTLIDLKTGWFTLLYEIRLKPEKAAEWEIHFAGQQTEFKILSLHPGQKYLVQVRCKPDHGYWSAWSPATFIQIPS 228
               SCOP domains d3d48r1 R:2-100 automated matches                                                                  d3d48r2 R:101-      204 automated matches                                                                SCOP domains
               CATH domains 3d48R01 R:2-101 Immunoglobulins                                                                     3d48R02 R:102      -204 Immunoglobulins                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee......eeeeeeeee......eeeeeeee......ee..........eeeehhhhh....eeeeeeeeee..eeee...eeee.hhh......eeeeee..------..eeeeee.............eeeeeeeee......eeeeee...eeee..--...eeeeeeeeee...........eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------V---------------------------------------------------------------------L-----------------------------------------R---------------- SAPs(SNPs)
                PROSITE (1) -FN3  PDB: R:3-104 UniProt: 27-128                                                                     FN3  PDB: R:105-204 UniProt: 129-229                                                                 PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------HEMATOPO_REC_L_F1  PDB: R:123-200 UniProt: 147-224                            ---- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d48 R   2 LPPGKPEIFKCRSPNKETFTCWWRPGTDGGLPTNYSLTYHREGETLMHECPDYITGGPNSCHFGKQYTSMWRTYIMMVNATNQMGSSFSDELYVDVTYIVQPDPPLELAVEVK------PYLWIKWSPPTLIDLKTGWFTLLYEIRLKPEKAAEWEIHFAGQQTEFKILS--PGQKYLVQVRCKPDHGYWSAWSPATFIQIPS 204
                                    11        21        31        41        51        61        71        81        91       101       111  |    121       131       141       151       161       171  |    181       191       201   
                                                                                                                                          114    121                                               171  |                              
                                                                                                                                                                                                      174

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: 4-helical cytokines (168)

Superfamily: 4-helical cytokines (168)

Family: Long-chain cytokines (46)

Protein domain: Prolactin (placental lactogen) (4)

Human (Homo sapiens) [TaxId: 9606] (3)

d3d48p_

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Fibronectin type III (212)

Family: Fibronectin type III (180)

Protein domain: automated matches (23)

Human (Homo sapiens) [TaxId: 9606] (23)

2a	d3d48r1	R:2-100
2b	d3d48r2	R:101-204

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Growth Hormone; Chain: A; (136)

Homologous Superfamily: [code=1.20.1250.10, no name defined] (130)

Human (Homo sapiens) (110)

3d48P00

P:13-198

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

2a	3d48R01	R:2-101
2b	3d48R02	R:102-204

(no "Pfam Domain" information available for 3D48)

Asymmetric/Biological Unit(hide GO term definitions)

Chain P (PRL_HUMAN | P01236)

molecular function
	GO:0005179	hormone activity	The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
	GO:0005148	prolactin receptor binding	Interacting selectively and non-covalently with the prolactin receptor.
	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:0060397	JAK-STAT cascade involved in growth hormone signaling pathway	The process in which STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of physiological ligands to the growth hormone receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	GO:0007565	female pregnancy	The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
	GO:0007595	lactation	The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
	GO:0046427	positive regulation of JAK-STAT cascade	Any process that activates or increases the frequency, rate or extent of the JAK-STAT signaling pathway activity.
	GO:0040014	regulation of multicellular organism growth	Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size.
cellular component
	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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Chain R (PRLR_HUMAN | P16471)

molecular function
	GO:0004896	cytokine receptor activity	Combining with a cytokine and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0042978	ornithine decarboxylase activator activity	Upregulation of the activity of the enzyme ornithine decarboxylase.
	GO:0017046	peptide hormone binding	Interacting selectively and non-covalently with any peptide with hormonal activity in animals.
	GO:0004925	prolactin receptor activity	Combining with prolactin and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0007259	JAK-STAT cascade	Any process in which STAT proteins (Signal Transducers and Activators of Transcription) and JAK (Janus Activated Kinase) proteins convey a signal to trigger a change in the activity or state of a cell. The JAK-STAT cascade begins with activation of STAT proteins by members of the JAK family of tyrosine kinases, proceeds through dimerization and subsequent nuclear translocation of STAT proteins, and ends with regulation of target gene expression by STAT proteins.
	GO:0060397	JAK-STAT cascade involved in growth hormone signaling pathway	The process in which STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of physiological ligands to the growth hormone receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes.
	GO:0042110	T cell activation	The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	GO:0007171	activation of transmembrane receptor protein tyrosine kinase activity	Any process that initiates the activity of the inactive transmembrane receptor protein tyrosine kinase activity.
	GO:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0007566	embryo implantation	Attachment of the blastocyst to the uterine lining.
	GO:0007595	lactation	The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
	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:0060644	mammary gland epithelial cell differentiation	The process in which a relatively unspecialized epithelial cell becomes a more specialized epithelial cell of the mammary gland.
	GO:0061180	mammary gland epithelium development	The process whose specific outcome is the progression of the mammary gland epithelium over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0038161	prolactin signaling pathway	A series of molecular signals initiated by the binding of the peptide hormone prolactin to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0060736	prostate gland growth	The increase in size or mass of the prostate gland where the increase in size or mass has the specific outcome of the progression of the gland, from its formation to its mature state.
	GO:0030155	regulation of cell adhesion	Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.
	GO:0030856	regulation of epithelial cell differentiation	Any process that modulates the frequency, rate or extent of epithelial cell differentiation.
	GO:0006694	steroid biosynthetic process	The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0031904	endosome lumen	The volume enclosed by the membrane of an endosome.
	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: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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	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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	3d48
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	PRL_HUMAN \| P01236
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Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (3, 3)

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