3AQE - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Biological Unit 7 (Jmol Viewer)

Biological Unit 8 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN RAMP2

Authors :   S. Kusano, M. Kukimoto-Niino, M. Shirouzu, T. Shindo, S. Yokoyama

Date :   29 Oct 10 (Deposition) - 09 Nov 11 (Release) - 25 Jul 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: E  (1x)
Biol. Unit 6: F  (1x)
Biol. Unit 7: A,B,C  (1x)
Biol. Unit 8: D,E,F  (1x)

Keywords :   Transmembrane, Gpcr, Adrenomedullin, Trafficking, Clr, Cgrp, Endoplasmic Reticulum, Disease, Neovascularization, Helix Bundle, Calcitonin Receptor-Like Receptor (Crlr), Endoplasmic Reticulum (Er), Cell Membrane, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Kusano, M. Kukimoto-Niino, N. Hino, N. Ohsawa, K. Okuda, K. Sakamoto, M. Shirouzu, T. Shindo, S. Yokoyama
Structural Basis For Extracellular Interactions Between Calcitonin Receptor-Like Receptor And Receptor Activity-Modifying Protein 2 For Adrenomedullin-Specific Binding
Protein Sci. V. 21 199 2012
PubMed-ID: 22102369 | Reference-DOI: 10.1002/PRO.2003

Molecule 1 - RECEPTOR ACTIVITY-MODIFYING PROTEIN 2
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI CELL-FREE SYSTEM
	Expression System Plasmid	:	PX070809-03
	Expression System Vector Type	:	PLASMID
	Fragment	:	EXTRACELLULAR DOMAIN, UNP RESIDUES 56-139
	Gene	:	RAMP2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CALCITONIN-RECEPTOR-LIKE RECEPTOR ACTIVITY-MODIFYING PROTEIN 2, CRLR ACTIVITY-MODIFYING PROTEIN 2

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:					E
Biological Unit 6 (1x)	:						F
Biological Unit 7 (1x)	:	A	B	C
Biological Unit 8 (1x)	:				D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 5 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 6 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 7 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 8 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3AQE)

Asymmetric Unit

No.	Residues
1	A:68	-	A:99
2	A:84	-	A:131
3	B:68	-	B:99
4	B:84	-	B:131
5	C:68	-	C:99
6	C:84	-	C:131
7	D:68	-	D:99
8	D:84	-	D:131
9	E:68	-	E:99
10	E:84	-	E:131
11	F:68	-	F:99
12	F:84	-	F:131

Asymmetric Unit

No.	Residues
1	Phe A:111	-	Pro A:112
2	Phe B:111	-	Pro B:112
3	Phe C:111	-	Pro C:112
4	Phe D:111	-	Pro D:112
5	Phe E:111	-	Pro E:112
6	Phe F:111	-	Pro F:112

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

(no "PROSITE Motif" information available for 3AQE)

(no "Exon" information available for 3AQE)

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:76
 aligned with RAMP2_HUMAN | O60895 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:76
                                    69        79        89        99       109       119       129      
          RAMP2_HUMAN    60 NYETAVQFCWNHYKDQMDPIEKDWCDWAMISRPYSTLRDCLEHFAELFDLGFPNPLAERIIFETHQIHFANCSLVQ 135
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 3aqe A  60 NYETAVQFCWNHYKDQmDPIEKDWCDWAmISRPYSTLRDCLEHFAELFDLGFPNPLAERIIFETHQIHFANCSLVQ 135
                                    69      | 79        89        99       109       119       129      
                                           76-MSE      88-MSE

Chain B from PDB  Type:PROTEIN  Length:76
 aligned with RAMP2_HUMAN | O60895 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:76
                                    69        79        89        99       109       119       129      
          RAMP2_HUMAN    60 NYETAVQFCWNHYKDQMDPIEKDWCDWAMISRPYSTLRDCLEHFAELFDLGFPNPLAERIIFETHQIHFANCSLVQ 135
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 3aqe B  60 NYETAVQFCWNHYKDQmDPIEKDWCDWAmISRPYSTLRDCLEHFAELFDLGFPNPLAERIIFETHQIHFANCSLVQ 135
                                    69      | 79        89        99       109       119       129      
                                           76-MSE      88-MSE

Chain C from PDB  Type:PROTEIN  Length:73
 aligned with RAMP2_HUMAN | O60895 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:73
                                    69        79        89        99       109       119       129   
          RAMP2_HUMAN    60 NYETAVQFCWNHYKDQMDPIEKDWCDWAMISRPYSTLRDCLEHFAELFDLGFPNPLAERIIFETHQIHFANCS 132
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 3aqe C  60 NYETAVQFCWNHYKDQmDPIEKDWCDWAmISRPYSTLRDCLEHFAELFDLGFPNPLAERIIFETHQIHFANCS 132
                                    69      | 79        89        99       109       119       129   
                                           76-MSE      88-MSE

Chain D from PDB  Type:PROTEIN  Length:74
 aligned with RAMP2_HUMAN | O60895 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:74
                                    69        79        89        99       109       119       129    
          RAMP2_HUMAN    60 NYETAVQFCWNHYKDQMDPIEKDWCDWAMISRPYSTLRDCLEHFAELFDLGFPNPLAERIIFETHQIHFANCSL 133
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 3aqe D  60 NYETAVQFCWNHYKDQmDPIEKDWCDWAmISRPYSTLRDCLEHFAELFDLGFPNPLAERIIFETHQIHFANCSL 133
                                    69      | 79        89        99       109       119       129    
                                           76-MSE      88-MSE

Chain E from PDB  Type:PROTEIN  Length:76
 aligned with RAMP2_HUMAN | O60895 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:76
                                    69        79        89        99       109       119       129      
          RAMP2_HUMAN    60 NYETAVQFCWNHYKDQMDPIEKDWCDWAMISRPYSTLRDCLEHFAELFDLGFPNPLAERIIFETHQIHFANCSLVQ 135
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 3aqe E  60 NYETAVQFCWNHYKDQmDPIEKDWCDWAmISRPYSTLRDCLEHFAELFDLGFPNPLAERIIFETHQIHFANCSLVQ 135
                                    69      | 79        89        99       109       119       129      
                                           76-MSE      88-MSE

Chain F from PDB  Type:PROTEIN  Length:75
 aligned with RAMP2_HUMAN | O60895 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:75
                                    69        79        89        99       109       119       129     
          RAMP2_HUMAN    60 NYETAVQFCWNHYKDQMDPIEKDWCDWAMISRPYSTLRDCLEHFAELFDLGFPNPLAERIIFETHQIHFANCSLV 134
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 3aqe F  60 NYETAVQFCWNHYKDQmDPIEKDWCDWAmISRPYSTLRDCLEHFAELFDLGFPNPLAERIIFETHQIHFANCSLV 134
                                    69      | 79        89        99       109       119       129     
                                           76-MSE      88-MSE

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 3AQE)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (RAMP2_HUMAN | O60895)

molecular function
	GO:0015026	coreceptor activity	Combining with an extracellular or intracellular messenger, and in cooperation with a nearby primary receptor, initiating 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:0008565	protein transporter activity	Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
	GO:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	GO:0034333	adherens junction assembly	The aggregation, arrangement and bonding together of a set of components to form an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments.
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0070831	basement membrane assembly	The aggregation, arrangement and bonding together of a set of components to form a basement membrane, a part of the extracellular region that consists of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue.
	GO:0070830	bicellular tight junction assembly	The aggregation, arrangement and bonding together of a set of components to form a tight junction, an occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet.
	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:0006816	calcium ion transport	The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0032870	cellular response to hormone stimulus	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 hormone stimulus.
	GO:0035924	cellular response to vascular endothelial growth factor stimulus	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 vascular endothelial growth factor stimulus.
	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:0007507	heart development	The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	GO:0006886	intracellular protein transport	The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
	GO:2000352	negative regulation of endothelial cell apoptotic process	Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process.
	GO:0043116	negative regulation of vascular permeability	Any process that reduces the extent to which blood vessels can be pervaded by fluid.
	GO:0045766	positive regulation of angiogenesis	Any process that activates or increases angiogenesis.
	GO:0030819	positive regulation of cAMP biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:2001214	positive regulation of vasculogenesis	Any process that activates or increases the frequency, rate or extent of vasculogenesis.
	GO:0072659	protein localization to plasma membrane	A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0031623	receptor internalization	A receptor-mediated endocytosis process that results in the movement of receptors from the plasma membrane to the inside of the cell. The process begins when cell surface receptors are monoubiquitinated following ligand-induced activation. Receptors are subsequently taken up into endocytic vesicles from where they are either targeted to the lysosome or vacuole for degradation or recycled back to the plasma membrane.
	GO:0008277	regulation of G-protein coupled receptor protein signaling pathway	Any process that modulates the frequency, rate or extent of G-protein coupled receptor protein signaling pathway activity.
	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:0032355	response to estradiol	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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
	GO:0001666	response to hypoxia	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 indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0032570	response to progesterone	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 progesterone stimulus.
	GO:0002040	sprouting angiogenesis	The extension of new blood vessels from existing capillaries into avascular tissues resulting from the proliferation of blood vessel endothelial cells.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
	GO:0097084	vascular smooth muscle cell development	The process aimed at the progression of a vascular smooth muscle cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. A vascular smooth muscle cell is a non-striated, elongated, spindle-shaped cell found lining the blood vessels.
	GO:0001570	vasculogenesis	The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005905	clathrin-coated pit	A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	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.
	GO:0043235	receptor complex	Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

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		Phe A:111 - Pro A:112	[ RasMol ]
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		Phe C:111 - Pro C:112	[ RasMol ]
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	3aqe
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	RAMP2_HUMAN \| O60895	:	2xvt 3aqf 4rwf

3aqf	CRYSTAL STRUCTURE OF THE HUMAN CRLR/RAMP2 EXTRACELLULAR COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 12)

Sites (0, 0)

SS Bonds (12, 12)

Cis Peptide Bonds (6, 6)

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