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- PDB-4rwf: Crystal structure of the CLR:RAMP2 extracellular domain heterodim... -

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Basic information

Entry
Database: PDB / ID: 4rwf
TitleCrystal structure of the CLR:RAMP2 extracellular domain heterodimer with bound adrenomedullin
Components
  • Adrenomedullin
  • Maltose transporter subunit, Receptor activity-modifying protein 2, Calcitonin gene-related peptide type 1 receptor fusion protein
KeywordsMEMBRANE PROTEIN/HORMONE / cell surface receptor / MEMBRANE PROTEIN-HORMONE complex
Function / homology
Function and homology information


adrenomedullin receptor binding / positive regulation of progesterone biosynthetic process / basement membrane assembly / cellular response to sucrose stimulus / adrenomedullin binding / CGRP receptor complex / neuron projection regeneration / adrenomedullin receptor activity / adrenomedullin receptor complex / vascular associated smooth muscle cell development ...adrenomedullin receptor binding / positive regulation of progesterone biosynthetic process / basement membrane assembly / cellular response to sucrose stimulus / adrenomedullin binding / CGRP receptor complex / neuron projection regeneration / adrenomedullin receptor activity / adrenomedullin receptor complex / vascular associated smooth muscle cell development / adrenomedullin receptor signaling pathway / calcitonin receptor activity / calcitonin gene-related peptide receptor signaling pathway / vascular associated smooth muscle cell proliferation / calcitonin gene-related peptide receptor activity / branching involved in labyrinthine layer morphogenesis / amylin receptor 2 signaling pathway / regulation of systemic arterial blood pressure / positive regulation of vasculogenesis / bicellular tight junction assembly / Calcitonin-like ligand receptors / response to ether / regulation of the force of heart contraction / regulation of G protein-coupled receptor signaling pathway / regulation of urine volume / G protein-coupled receptor internalization / adherens junction assembly / negative regulation of vascular permeability / sprouting angiogenesis / negative regulation of vasoconstriction / response to starvation / detection of maltose stimulus / maltose transport complex / odontogenesis of dentin-containing tooth / carbohydrate transport / androgen metabolic process / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / cellular response to vascular endothelial growth factor stimulus / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / developmental growth / animal organ regeneration / negative regulation of endothelial cell apoptotic process / vasculogenesis / positive regulation of heart rate / cellular response to hormone stimulus / response to glucocorticoid / coreceptor activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / clathrin-coated pit / positive regulation of vascular associated smooth muscle cell proliferation / ATP-binding cassette (ABC) transporter complex / protein localization to plasma membrane / female pregnancy / cell chemotaxis / intracellular protein transport / response to insulin / neural tube closure / G protein-coupled receptor activity / hormone activity / receptor internalization / regulation of blood pressure / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of angiogenesis / calcium ion transport / protein transport / cellular response to xenobiotic stimulus / outer membrane-bounded periplasmic space / heart development / positive regulation of cytosolic calcium ion concentration / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / secretory granule lumen / G alpha (s) signalling events / angiogenesis / response to lipopolysaccharide / periplasmic space / response to hypoxia / lysosome / cell population proliferation / receptor complex / cell surface receptor signaling pathway / endosome / G protein-coupled receptor signaling pathway / positive regulation of apoptotic process / inflammatory response / signaling receptor binding / negative regulation of cell population proliferation / positive regulation of cell population proliferation / DNA damage response / positive regulation of gene expression / cell surface / endoplasmic reticulum / signal transduction / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Pro-adrenomedullin / : / GPCR, family 2, calcitonin gene-related peptide, type 1 receptor / Receptor activity modifying protein / RAMP domain superfamily / Receptor activity modifying family / GPCR, family 2, calcitonin receptor family / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP family / G-protein coupled receptors family 2 signature 1. ...Pro-adrenomedullin / : / GPCR, family 2, calcitonin gene-related peptide, type 1 receptor / Receptor activity modifying protein / RAMP domain superfamily / Receptor activity modifying family / GPCR, family 2, calcitonin receptor family / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP family / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / 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. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Receptor activity-modifying protein 2 / Maltose/maltodextrin-binding periplasmic protein / Pro-adrenomedullin / Calcitonin gene-related peptide type 1 receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 Å
AuthorsBooe, J. / Pioszak, A.
CitationJournal: Mol.Cell / Year: 2015
Title: Structural Basis for Receptor Activity-Modifying Protein-Dependent Selective Peptide Recognition by a G Protein-Coupled Receptor.
Authors: Booe, J.M. / Walker, C.S. / Barwell, J. / Kuteyi, G. / Simms, J. / Jamaluddin, M.A. / Warner, M.L. / Bill, R.M. / Harris, P.W. / Brimble, M.A. / Poyner, D.R. / Hay, D.L. / Pioszak, A.A.
History
DepositionDec 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose transporter subunit, Receptor activity-modifying protein 2, Calcitonin gene-related peptide type 1 receptor fusion protein
B: Adrenomedullin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2148
Polymers69,5612
Non-polymers6536
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint8 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.454, 84.283, 115.764
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsASU contains the biological heterodimer

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Components

#1: Protein Maltose transporter subunit, Receptor activity-modifying protein 2, Calcitonin gene-related peptide type 1 receptor fusion protein


Mass: 66308.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, CE10_4748, RAMP2, CALCRL, CGRPR / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B DE3
References: UniProt: P0AEX9, UniProt: O60895, UniProt: Q16602
#2: Protein/peptide Adrenomedullin / CGRP type 1 receptor / Calcitonin receptor-like receptor


Mass: 3252.657 Da / Num. of mol.: 1 / Fragment: residues 119-146 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P35318
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 19% PEG3350 0.1 M Tris-HCl, pH 8.3 225 mM Sodium Acetate 20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 70118 / Num. obs: 70048 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.068 / Χ2: 1.023 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.76-1.7950.96633910.496198.2
1.79-1.826.20.86634260.518199.5
1.82-1.867.20.69334450.5271100
1.86-1.97.40.55734600.561100
1.9-1.947.50.44235050.5651100
1.94-1.987.50.3534540.6031100
1.98-2.037.50.26434660.651100
2.03-2.097.50.22734780.6641100
2.09-2.157.50.17834570.7281100
2.15-2.227.50.15534850.7811100
2.22-2.37.50.13834810.91100
2.3-2.397.50.1235131.0341100
2.39-2.57.50.10934791.1321100
2.5-2.637.50.09235241.2411100
2.63-2.797.50.07734811.3081100
2.79-3.017.40.0735411.5511100
3.01-3.317.40.05935311.8471100
3.31-3.797.40.05635611.8141100
3.79-4.787.30.04236051.6531100
4.78-506.90.03937651.517199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
MD2diffractometerdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.551 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2003 3470 5 %RANDOM
Rwork0.1569 ---
obs0.159 66505 99.86 %-
all-66598 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.49 Å2 / Biso mean: 36.41 Å2 / Biso min: 17.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---0.2 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4540 0 43 394 4977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.024741
X-RAY DIFFRACTIONr_bond_other_d0.0010.024388
X-RAY DIFFRACTIONr_angle_refined_deg1.9291.9486442
X-RAY DIFFRACTIONr_angle_other_deg0.961310142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1075580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47525.435230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73915775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9791515
X-RAY DIFFRACTIONr_chiral_restr0.1290.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021081
X-RAY DIFFRACTIONr_mcbond_it1.7411.9042300
X-RAY DIFFRACTIONr_mcbond_other1.7411.9042298
X-RAY DIFFRACTIONr_mcangle_it2.4282.8422873
LS refinement shellResolution: 1.76→1.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 257 -
Rwork0.284 4766 -
all-5023 -
obs--98.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2672-0.1608-0.7161.7943-0.35931.6824-0.13580.0065-0.05230.15710.05940.27970.0847-0.26210.07640.0366-0.0030.03580.1259-0.04180.0682-27.24580.9137-13.0384
23.79332.7661-0.99154.7066-0.9381.5067-0.06110.0374-0.292-0.2686-0.0646-0.30270.1400.12570.04040.01720.01520.0126-0.00110.02834.779212.6605-27.7056
32.10720.2480.34452.61110.85515.2081-0.0166-0.34220.22280.1297-0.1679-0.0509-0.1275-0.10370.18460.0282-0.0051-0.01930.062-0.03190.03574.128427.1669-15.054
46.2826-0.67252.6263.1919-2.21568.7493-0.021-0.15790.2427-0.01930.02290.5736-0.3948-0.8082-0.00190.1072-0.00290.01540.2052-0.10470.1776-10.09725.4898-17.8042
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 374
2X-RAY DIFFRACTION1A2201 - 2206
3X-RAY DIFFRACTION2A1055 - 1139
4X-RAY DIFFRACTION3A2032 - 2129
5X-RAY DIFFRACTION4B35 - 53

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