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(-) Description

Title :  CRYSTAL STRUCTURE OF HORMONE RECEPTOR
 
Authors :  X. -L. He, D. -C. Chow, M. M. Martick, K. C. Garcia
Date :  14 Jun 01  (Deposition) - 05 Sep 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Natriuretic Peptide Receptor, Dimer, Allosteric Activation, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. L. He, D. C. Chow, M. M. Martick, K. C. Garcia
Allosteric Activation Of A Spring-Loaded Natriuretic Peptid Receptor Dimer By Hormone.
Science V. 293 1657 2001
PubMed-ID: 11533490  |  Reference-DOI: 10.1126/SCIENCE.1062246

(-) Compounds

Molecule 1 - ATRIAL NATRIURETIC PEPTIDE CLEARANCE RECEPTOR
    ChainsA
    EngineeredYES
    Expression SystemDROSOPHILA MELANOGASTER
    Expression System CommonFRUIT FLY
    Expression System PlasmidPRMHA3
    Expression System StrainS2
    Expression System Taxid7227
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNPR-C

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 13)

Asymmetric Unit (6, 13)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2CL2Ligand/IonCHLORIDE ION
3FUC1Ligand/IonALPHA-L-FUCOSE
4MAN2Ligand/IonALPHA-D-MANNOSE
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 1 (5, 22)
No.NameCountTypeFull Name
1BMA8Ligand/IonBETA-D-MANNOSE
2CL-1Ligand/IonCHLORIDE ION
3FUC2Ligand/IonALPHA-L-FUCOSE
4MAN4Ligand/IonALPHA-D-MANNOSE
5NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NDG4Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:248 , LEU A:279 , LEU A:280 , ARG A:281 , THR A:282 , GLU A:314 , NDG A:441BINDING SITE FOR RESIDUE NDG A 440
02AC2SOFTWAREARG A:281 , THR A:282 , VAL A:283 , GLU A:288 , NDG A:440 , BMA A:442BINDING SITE FOR RESIDUE NDG A 441
03AC3SOFTWAREVAL A:283 , NDG A:441 , MAN A:443 , BMA A:445BINDING SITE FOR RESIDUE BMA A 442
04AC4SOFTWAREGLU A:288 , BMA A:442 , BMA A:444BINDING SITE FOR RESIDUE MAN A 443
05AC5SOFTWAREGLU A:288 , MET A:292 , MAN A:443BINDING SITE FOR RESIDUE BMA A 444
06AC6SOFTWAREBMA A:442BINDING SITE FOR RESIDUE BMA A 445
07AC7SOFTWAREHIS A:328 , LEU A:331 , ARG A:332 , THR A:351 , LYS A:393 , NAG A:447 , NAG A:448BINDING SITE FOR RESIDUE FUC A 446
08AC8SOFTWARELEU A:331 , ARG A:332 , ASN A:349 , ALA A:363 , FUC A:446 , NAG A:448BINDING SITE FOR RESIDUE NAG A 447
09AC9SOFTWAREGLY A:334 , FUC A:446 , NAG A:447 , MAN A:449BINDING SITE FOR RESIDUE NAG A 448
10BC1SOFTWARENAG A:448 , BMA A:450BINDING SITE FOR RESIDUE MAN A 449
11BC2SOFTWAREMAN A:449BINDING SITE FOR RESIDUE BMA A 450
12BC3SOFTWAREPRO A:15 , PHE A:22 , SER A:61 , PRO A:89 , VAL A:90 , CYS A:91BINDING SITE FOR RESIDUE CL A 451
13BC4SOFTWAREARG A:66 , HIS A:104BINDING SITE FOR RESIDUE CL A 452

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:63 -A:91
2A:168 -A:216

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:88 -Pro A:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ANF_RECEPTORSPS00458 Natriuretic peptides receptors signature.ANPRC_HUMAN133-150  1A:88-105
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ANF_RECEPTORSPS00458 Natriuretic peptides receptors signature.ANPRC_HUMAN133-150  2A:88-105

(-) Exons   (6, 6)

Asymmetric Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3aENST000002650743aENSE00001917259chr5:32711540-327126511112ANPRC_HUMAN1-2572571A:5-212 (gaps)208
1.5ENST000002650745ENSE00000735248chr5:32724804-32724926123ANPRC_HUMAN257-298421A:212-25342
1.6ENST000002650746ENSE00000971354chr5:32738970-32739136167ANPRC_HUMAN298-353561A:253-30856
1.7ENST000002650747ENSE00002059415chr5:32774814-32774949136ANPRC_HUMAN354-399461A:309-35446
1.8ENST000002650748ENSE00001082097chr5:32780828-3278092295ANPRC_HUMAN399-430321A:354-38532
1.9aENST000002650749aENSE00002167695chr5:32782999-32783134136ANPRC_HUMAN431-476461A:386-41833
1.10aENST0000026507410aENSE00001164694chr5:32784902-3278498988ANPRC_HUMAN476-505300--
1.11dENST0000026507411dENSE00001938989chr5:32786340-32787256917ANPRC_HUMAN505-541370--

(-) Sequences/Alignments

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:407
 aligned with ANPRC_HUMAN | P17342 from UniProtKB/Swiss-Prot  Length:541

    Alignment length:414
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459    
          ANPRC_HUMAN    50 PQKIEVLVLLPQDDSYLFSLTRVRPAIEYALRSVEGNGTGRRLLPPGTRFQVAYEDSDCGNRALFSLVDRVAAARGAKPDLILGPVCEYAAAPVARLASHWDLPMLSAGALAAGFQHKDSEYSHLTRVAPAYAKMGEMMLALFRHHHWSRAALVYSDDKLERNCYFTLEGVHEVFQEEGLHTSIYSFDETKDLDLEDIVRNIQASERVVIMCASSDTIRSIMLVAHRHGMTSGDYAFFNIELFNSSSYGDGSWKRGDKHDFEAKQAYSSLQTVTLLRTVKPEFEKFSMEVKSSVEKQGLNMEDYVNMFVEGFHDAILLYVLALHEVLRAGYSKKDGGKIIQQTWNRTFEGIAGQVSIDANGDRYGDFSVIAMTDVEAGTQEVIGDYFGKEGRFEMRPNVKYPWGPLKLRIDENR 463
               SCOP domains d1jdna_ A: Hormone binding domain of        the atrial natriuretic peptide receptor                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1jdnA02 A:5-134,A:284-368  [code=3.4       0.50.2300, no name defined]                                                            1jdnA01 A:135-281,A:369-400  [code=3.40.50.2300, no name defined]                                                                                  --1jdnA02 A:5-134,A:284-368  [code=3.40.50.2300, no name defined]                      1jdnA01 A:135-281,A:369-400     ------------------ CATH domains
               Pfam domains ---------------------ANF_receptor-1j       dnA01 A:26-379                                                                                                                                                                                                                                                                                                                              --------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee........hhhhhhhhhhhhhhhhh.-------......eeeeeee....hhhhhhhhhhhhhh......eee...hhhhhhhhhhhhhhh...eee....hhhhhh.......eee....hhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh.......eeeee.hhhhhhhh.........hhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh.eeeee..eeeee........eeeeeeeee....eeeeeeeee....eeee........hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------ANF_RECEPTORS     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: A:5-212 (gaps) UniProt: 1-257 [INCOMPLETE]                                                                                                                                                      ----------------------------------------Exon 1.6  PDB: A:253-308 UniProt: 298-353               Exon 1.7  PDB: A:309-354 UniProt: 354-399     -------------------------------Exon 1.9a  PDB: A:386-418         Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.5  PDB: A:212-253 UniProt: 257-298 ----------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:354-385        --------------------------------- Transcript 1 (2)
                 1jdn A   5 PQKIEVLVLLPQDDSYLFSLTRVRPAIEYALRSVEG-------LPPGTRFQVAYEDSDCGNRALFSLVDRVAAARGAKPDLILGPVCEYAAAPVARLASHWDLPMLSAGALAAGFQHKDSEYSHLTRVAPAYAKMGEMMLALFRHHHWSRAALVYSDDKLERNCYFTLEGVHEVFQEEGLHTSIYSFDETKDLDLEDIVRNIQASERVVIMCASSDTIRSIMLVAHRHGMTSGDYAFFNIELFNSSSYGDGSWKRGDKHDFEAKQAYSSLQTVTLLRTVKPEFEKFSMEVKSSVEKQGLNMEDYVNMFVEGFHDAILLYVLALHEVLRAGYSKKDGGKIIQQTWNRTFEGIAGQVSIDANGDRYGDFSVIAMTDVEAGTQEVIGDYFGKEGRFEMRPNVKYPWGPLKLRIDENR 418
                                    14        24        34     |   -   |    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414    
                                                              40      48                                                                                                                                                                                                                                                                                                                                                                                  

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A   (ANPRC_HUMAN | P17342)
molecular function
    GO:0008528    G-protein coupled peptide receptor activity    Combining with a peptide and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
    GO:0004016    adenylate cyclase activity    Catalysis of the reaction: ATP = 3',5'-cyclic AMP + diphosphate.
    GO:0042562    hormone binding    Interacting selectively and non-covalently with any hormone, naturally occurring substances secreted by specialized cells that affect the metabolism or behavior of other cells possessing functional receptors for the hormone.
    GO:0016941    natriuretic peptide receptor activity    Combining with a natriuretic peptide and transmitting the signal to initiate a change in cell activity.
    GO:0017046    peptide hormone binding    Interacting selectively and non-covalently with any peptide with hormonal activity in animals.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0007189    adenylate cyclase-activating G-protein coupled receptor signaling pathway    The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds through activation of adenylyl cyclase activity and a subsequent increase in the concentration of cyclic AMP (cAMP).
    GO:0007193    adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway    The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds through inhibition of adenylyl cyclase activity and a subsequent decrease in the concentration of cyclic AMP (cAMP).
    GO:0006171    cAMP biosynthetic process    The chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0019933    cAMP-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via cyclic AMP (cAMP). Includes production of cAMP, and downstream effectors that further transmit the signal within the cell.
    GO:0009190    cyclic nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue.
    GO:0048662    negative regulation of smooth muscle cell proliferation    Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation.
    GO:0002158    osteoclast proliferation    The multiplication or reproduction of osteoclasts, resulting in the expansion of an osteoclast cell population. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes.
    GO:0030157    pancreatic juice secretion    The regulated release of pancreatic juice by the exocrine pancreas into the upper part of the intestine. Pancreatic juice is slightly alkaline and contains numerous enzymes and inactive enzyme precursors including alpha-amylase, chymotrypsinogen, lipase, procarboxypeptidase, proelastase, prophospholipase A2, ribonuclease, and trypsinogen. Its high concentration of bicarbonate ions helps to neutralize the acid from the stomach.
    GO:0048015    phosphatidylinositol-mediated signaling    A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0007200    phospholipase C-activating G-protein coupled receptor signaling pathway    The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds with activation of phospholipase C (PLC) and a subsequent increase in the concentration of inositol trisphosphate (IP3) and diacylglycerol (DAG).
    GO:0051000    positive regulation of nitric-oxide synthase activity    Any process that activates or increases the activity of the enzyme nitric-oxide synthase.
    GO:0035810    positive regulation of urine volume    Any process that increases the amount of urine excreted from the body over a unit of time.
    GO:0008217    regulation of blood pressure    Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
    GO:0033688    regulation of osteoblast proliferation    Any process that modulates the frequency, rate or extent of osteoblast proliferation.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
cellular component
    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: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: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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ANPRC_HUMAN | P173421jdp 1yk0 1yk1

(-) Related Entries Specified in the PDB File

1jdp 1JDP CONTAINS THE LIGANDED RECEPTOR.