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- PDB-3aqf: Crystal structure of the human CRLR/RAMP2 extracellular complex -

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Basic information

Entry
Database: PDB / ID: 3aqf
TitleCrystal structure of the human CRLR/RAMP2 extracellular complex
Components
  • Calcitonin gene-related peptide type 1 receptor
  • Receptor activity-modifying protein 2
KeywordsTRANSPORT PROTEIN/MEMBRANE PROTEIN / Transmembrane / GPCR / Adrenomedullin / TRAFFICKING / CLR / CGRP / Endoplasmic Reticulum / AM-receptor / DISEASE / Neovascularization / Co-activating receptor for Adrenomedullin / Adrenomedullin (AM) / Endoplasmic Reticulum (ER) / TRANSPORT PROTEIN-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


basement membrane assembly / vascular associated smooth muscle cell development / CGRP receptor complex / calcitonin gene-related peptide receptor signaling pathway / adrenomedullin binding / cellular response to sucrose stimulus / adrenomedullin receptor activity / adrenomedullin receptor complex / adrenomedullin receptor signaling pathway / calcitonin receptor activity ...basement membrane assembly / vascular associated smooth muscle cell development / CGRP receptor complex / calcitonin gene-related peptide receptor signaling pathway / adrenomedullin binding / cellular response to sucrose stimulus / adrenomedullin receptor activity / adrenomedullin receptor complex / adrenomedullin receptor signaling pathway / calcitonin receptor activity / vascular associated smooth muscle cell proliferation / calcitonin gene-related peptide receptor activity / Calcitonin-like ligand receptors / positive regulation of vasculogenesis / bicellular tight junction assembly / regulation of G protein-coupled receptor signaling pathway / adherens junction assembly / negative regulation of vascular permeability / sprouting angiogenesis / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / coreceptor activity / negative regulation of endothelial cell apoptotic process / clathrin-coated pit / cellular response to hormone stimulus / positive regulation of vascular associated smooth muscle cell proliferation / G protein-coupled receptor activity / protein localization to plasma membrane / intracellular protein transport / adenylate cyclase-activating G protein-coupled receptor signaling pathway / receptor internalization / regulation of blood pressure / positive regulation of angiogenesis / calcium ion transport / protein transport / heart development / G alpha (s) signalling events / angiogenesis / lysosome / cell surface receptor signaling pathway / receptor complex / endosome / G protein-coupled receptor signaling pathway / positive regulation of gene expression / cell surface / endoplasmic reticulum / plasma membrane / cytoplasm
Similarity search - Function
Receptor activity modifying family / GPCR, family 2, calcitonin gene-related peptide, type 1 receptor / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / Receptor activity modifying protein / RAMP domain superfamily / Receptor activity modifying family / GPCR, family 2, calcitonin receptor family / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain ...Receptor activity modifying family / GPCR, family 2, calcitonin gene-related peptide, type 1 receptor / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / Receptor activity modifying protein / RAMP domain superfamily / Receptor activity modifying family / GPCR, family 2, calcitonin receptor family / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / DNA polymerase; domain 1 / Few Secondary Structures / Irregular / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Receptor activity-modifying protein 2 / Calcitonin gene-related peptide type 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsKusano, S. / Kukimono-Niino, M. / Shirouzu, M. / Shindo, T. / Yokoyama, S.
CitationJournal: Protein Sci. / Year: 2012
Title: Structural basis for extracellular interactions between calcitonin receptor-like receptor and receptor activity-modifying protein 2 for adrenomedullin-specific binding
Authors: Kusano, S. / Kukimoto-Niino, M. / Hino, N. / Ohsawa, N. / Okuda, K. / Sakamoto, K. / Shirouzu, M. / Shindo, T. / Yokoyama, S.
History
DepositionOct 29, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor activity-modifying protein 2
B: Calcitonin gene-related peptide type 1 receptor


Theoretical massNumber of molelcules
Total (without water)24,6172
Polymers24,6172
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-10 kcal/mol
Surface area10170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.424, 55.424, 119.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Receptor activity-modifying protein 2 / Calcitonin-receptor-like receptor activity-modifying protein 2 / CRLR activity-modifying protein 2


Mass: 10581.471 Da / Num. of mol.: 1 / Fragment: Extracellular Domain, UNP residues 39-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAMP2 / Plasmid: PX070809-03 / Production host: Escherichia coli cell-free system / References: UniProt: O60895
#2: Protein Calcitonin gene-related peptide type 1 receptor / CGRP type 1 receptor / Calcitonin receptor-like receptor


Mass: 14035.874 Da / Num. of mol.: 1 / Fragment: N-terminal Domain, UNP residues 23-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALCRL, CGRPR / Plasmid: PX080331-02 / Production host: Escherichia coli cell-free system / References: UniProt: Q16602
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M bis-Tris, 30 % (v/v) PEG MME 550, 0.05M Calcium Chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9790, 0.9793, 0.9640
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 17, 2009
RadiationMonochromator: Si double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97931
30.9641
ReflectionResolution: 2.6→50 Å / Num. obs: 6157 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 32.4 Å2 / Rsym value: 0.115 / Net I/σ(I): 20.3
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 5.9 / Rsym value: 0.252 / % possible all: 91.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→40.62 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2821 662 10.7 %RANDOM
Rwork0.2221 5413 --
obs-6075 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.8801 Å2
Displacement parametersBiso mean: 34.2017 Å2
Baniso -1Baniso -2Baniso -3
1--6.674 Å20 Å20 Å2
2---6.674 Å20 Å2
3---13.348 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.6→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 0 30 1492
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.051.5
X-RAY DIFFRACTIONc_scbond_it3.4822
X-RAY DIFFRACTIONc_mcangle_it3.3092
X-RAY DIFFRACTIONc_scangle_it4.962.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 102 11.3 %
Rwork0.24 802 -
obs--90.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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