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- PDB-2yx8: Crystal structure of the extracellular domain of human RAMP1 -

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Basic information

Entry
Database: PDB / ID: 2yx8
TitleCrystal structure of the extracellular domain of human RAMP1
ComponentsReceptor activity-modifying protein 1
KeywordsPROTEIN TRANSPORT / TRANSMEMBRANE / DISEASE / MIGRAINE / TRAFFICKING / FOLDING / GPCR / CLR / CRLR / CGRP / ENDOPLASMIC RETICULUM / BIBN4096BS / GLYCOSYLATION / ADRENOMEDULIN / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


calcitonin gene-related peptide binding / CGRP receptor complex / calcitonin gene-related peptide receptor signaling pathway / positive regulation of protein glycosylation / amylin receptor activity / calcitonin gene-related peptide receptor activity / amylin receptor signaling pathway / Calcitonin-like ligand receptors / regulation of G protein-coupled receptor signaling pathway / coreceptor activity ...calcitonin gene-related peptide binding / CGRP receptor complex / calcitonin gene-related peptide receptor signaling pathway / positive regulation of protein glycosylation / amylin receptor activity / calcitonin gene-related peptide receptor activity / amylin receptor signaling pathway / Calcitonin-like ligand receptors / regulation of G protein-coupled receptor signaling pathway / coreceptor activity / cellular response to hormone stimulus / protein localization to plasma membrane / intracellular protein transport / adenylate cyclase-activating G protein-coupled receptor signaling pathway / receptor internalization / calcium ion transport / protein transport / G alpha (s) signalling events / angiogenesis / receptor complex / G protein-coupled receptor signaling pathway / cell surface / plasma membrane
Similarity search - Function
Receptor activity modifying family / Receptor activity modifying protein / RAMP domain superfamily / Receptor activity modifying family / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Receptor activity-modifying protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsKusano, S. / Kukimoto-Niino, M. / Shirouzu, M. / Shindo, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Protein Sci. / Year: 2008
Title: Crystal structure of the human receptor activity-modifying protein 1 extracellular domain.
Authors: Kusano, S. / Kukimoto-Niino, M. / Akasaka, R. / Toyama, M. / Terada, T. / Shirouzu, M. / Shindo, T. / Yokoyama, S.
History
DepositionApr 24, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor activity-modifying protein 1


Theoretical massNumber of molelcules
Total (without water)10,7821
Polymers10,7821
Non-polymers00
Water30617
1
A: Receptor activity-modifying protein 1

A: Receptor activity-modifying protein 1


Theoretical massNumber of molelcules
Total (without water)21,5642
Polymers21,5642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area1410 Å2
ΔGint-10 kcal/mol
Surface area9690 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.097, 43.097, 82.992
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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Components

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


Mass: 10781.900 Da / Num. of mol.: 1 / Fragment: Extracellular Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAMP1 / Plasmid: PE060926-03 / Production host: Escherichia coli (E. coli) / References: UniProt: O60894
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 1.88 Å3/Da / Density % sol: 31.159447 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M tri-Sodium Citrate Dihydrate, 0.15M di-Ammonium Citrate, 25% PEG3350, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9789, 0.9793, 0.9640
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 26, 2007
RadiationMonochromator: Si double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97931
30.9641
ReflectionResolution: 2.4→50 Å / Num. obs: 3371 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 15.15 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.095 / Net I/σ(I): 21.26
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2.59 / Rsym value: 0.33 / % possible all: 93.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→24.56 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1048459.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 333 9.9 %RANDOM
Rwork0.221 ---
obs-3350 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.2507 Å2 / ksol: 0.461846 e/Å3
Displacement parametersBiso mean: 36.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.49 Å20 Å20 Å2
2--3.49 Å20 Å2
3----6.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→24.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms667 0 0 17 684
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_improper_angle_d0.68
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 51 10.2 %
Rwork0.271 451 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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