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- PDB-6v2e: Crystal structure of the human CLR:RAMP2 extracellular domain het... -

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Basic information

Entry
Database: PDB / ID: 6v2e
TitleCrystal structure of the human CLR:RAMP2 extracellular domain heterodimer with bound high-affinity adrenomedullin S45R/K46L/S48G/Q50W variant
Components
  • ADM
  • Maltose/maltodextrin-binding periplasmic protein,Receptor activity-modifying protein 2,Calcitonin gene-related peptide type 1 receptor
KeywordsMEMBRANE PROTEIN / Class B GPCR / Peptide Hormone
Function / homology
Function and homology information


adrenomedullin receptor binding / positive regulation of progesterone biosynthetic process / basement membrane assembly / CGRP receptor complex / calcitonin gene-related peptide receptor signaling pathway / vascular associated smooth muscle cell development / adrenomedullin binding / cellular response to sucrose stimulus / neuron projection regeneration / adrenomedullin receptor activity ...adrenomedullin receptor binding / positive regulation of progesterone biosynthetic process / basement membrane assembly / CGRP receptor complex / calcitonin gene-related peptide receptor signaling pathway / vascular associated smooth muscle cell development / adrenomedullin binding / cellular response to sucrose stimulus / neuron projection regeneration / adrenomedullin receptor activity / adrenomedullin receptor complex / adrenomedullin receptor signaling pathway / calcitonin receptor activity / spongiotrophoblast layer development / vascular associated smooth muscle cell proliferation / calcitonin gene-related peptide receptor activity / Calcitonin-like ligand receptors / branching involved in labyrinthine layer morphogenesis / positive regulation of vasculogenesis / regulation of systemic arterial blood pressure / bicellular tight junction assembly / regulation of the force of heart contraction / regulation of G protein-coupled receptor signaling pathway / adherens junction assembly / G protein-coupled receptor internalization / regulation of urine volume / negative regulation of vascular permeability / sprouting angiogenesis / negative regulation of vasoconstriction / positive regulation of heart rate / detection of maltose stimulus / maltose binding / maltose transport complex / response to starvation / maltose transport / maltodextrin transmembrane transport / odontogenesis of dentin-containing tooth / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / cAMP-mediated signaling / androgen metabolic process / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / developmental growth / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / animal organ regeneration / coreceptor activity / negative regulation of endothelial cell apoptotic process / clathrin-coated pit / response to glucocorticoid / cellular response to hormone stimulus / positive regulation of vascular associated smooth muscle cell proliferation / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / neural tube closure / female pregnancy / G protein-coupled receptor activity / protein localization to plasma membrane / intracellular protein transport / response to insulin / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / receptor internalization / regulation of blood pressure / positive regulation of angiogenesis / calcium ion transport / protein transport / outer membrane-bounded periplasmic space / heart development / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / angiogenesis / response to lipopolysaccharide / lysosome / periplasmic space / response to hypoxia / cell surface receptor signaling pathway / receptor complex / endosome / inflammatory response / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / signaling receptor binding / DNA damage response / positive regulation of cell population proliferation / 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. / Hormone receptor domain ...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. / 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. / 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
Similarity search - Domain/homology
alpha-maltose / FORMIC ACID / AMINO GROUP / 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 / Resolution: 1.83 Å
AuthorsBooe, J.M. / Pioszak, A.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104251 United States
American Heart Association18PRE33990152 United States
CitationJournal: Acs Pharmacol Transl Sci / Year: 2020
Title: Picomolar Affinity Antagonist and Sustained Signaling Agonist Peptide Ligands for the Adrenomedullin and Calcitonin Gene-Related Peptide Receptors.
Authors: Booe, J.M. / Warner, M.L. / Pioszak, A.A.
History
DepositionNov 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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/maltodextrin-binding periplasmic protein,Receptor activity-modifying protein 2,Calcitonin gene-related peptide type 1 receptor
B: ADM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6657
Polymers68,1682
Non-polymers4965
Water10,845602
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-7 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.017, 84.993, 123.064
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AB

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Receptor activity-modifying protein 2,Calcitonin gene-related peptide type 1 receptor / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Calcitonin-receptor-like ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Calcitonin-receptor-like receptor activity-modifying protein 2 / CRLR activity-modifying protein 2 / CGRP type 1 receptor / Calcitonin receptor-like receptor


Mass: 66308.352 Da / Num. of mol.: 1 / Mutation: L106R,RAMP2 L106R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, b4034, JW3994, RAMP2, CALCRL, CGRPR / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEX9, UniProt: O60895, UniProt: Q16602
#2: Protein/peptide ADM


Mass: 1860.102 Da / Num. of mol.: 1 / Mutation: S45R, K46L, S48G, Q50W / 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

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Non-polymers , 3 types, 606 molecules

#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-NH2 / AMINO GROUP / Amine


Mass: 16.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 602 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 20% PEG MME 5000, 0.1 M sodium HEPEs pH 8.2, 150 mM sodium formate, 3% (v/v) dimethyl sulfoxide

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 63239 / % possible obs: 99.6 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.034 / Rrim(I) all: 0.093 / Χ2: 0.907 / Net I/σ(I): 6.8 / Num. measured all: 468938
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.83-1.866.91.1830640.6310.4761.2740.58998.9
1.86-1.97.31.00631200.6980.3961.0820.61599
1.9-1.937.50.79730990.8050.3090.8550.64699.1
1.93-1.977.50.64431140.8740.250.6910.66399.5
1.97-2.017.50.49131310.9160.190.5270.68299.6
2.01-2.067.50.41731320.9340.1620.4480.70399.4
2.06-2.117.50.3530810.9550.1360.3750.74499.4
2.11-2.177.50.28831530.9660.1120.310.74399.5
2.17-2.237.50.24431290.9750.0950.2610.76799.4
2.23-2.317.50.21631220.980.0840.2320.85999.5
2.31-2.397.50.18231520.9850.0710.1950.89499.7
2.39-2.487.50.15331510.990.0590.1640.92699.8
2.48-2.67.50.13131660.9910.0510.1410.96299.7
2.6-2.737.50.10231650.9950.040.1090.97199.9
2.73-2.97.50.08731620.9960.0340.0931.00499.8
2.9-3.137.50.07531910.9950.0290.0811.27399.8
3.13-3.447.40.06232030.9960.0240.0671.55799.8
3.44-3.947.40.04432150.9980.0180.0481.44199.9
3.94-4.977.30.03132730.9990.0120.0341.05699.9
4.97-506.90.02934160.9990.0120.0310.97199.6

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Processing

Software
NameVersionClassification
HKL-2000v.712data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000v.712data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RWF

4rwf


Resolution: 1.83→36.97 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.071 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.105
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1896 3235 5.1 %RANDOM
Rwork0.1565 ---
obs0.1582 59946 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.18 Å2 / Biso mean: 29.177 Å2 / Biso min: 14.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 1.83→36.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4529 0 33 602 5164
Biso mean--25.64 37.74 -
Num. residues----571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134803
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174313
X-RAY DIFFRACTIONr_angle_refined_deg1.531.6536550
X-RAY DIFFRACTIONr_angle_other_deg1.411.58710086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2715602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67724.303251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74615797
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8061517
X-RAY DIFFRACTIONr_chiral_restr0.0830.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02987
LS refinement shellResolution: 1.831→1.879 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 242 -
Rwork0.27 4263 -
all-4505 -
obs--97.17 %
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)
11.1673-0.3097-1.04271.4237-0.00042.1599-0.14880.0605-0.11740.03710.0176-0.00980.3383-0.12890.13120.0565-0.0260.0220.0315-0.02240.022-25.1222.063-12.724
23.31732.0387-1.59874.4783-1.08733.2027-0.10260.0123-0.299-0.130.0145-0.1230.1420.03670.08810.03030.01110.01680.0077-0.00510.06195.23614.132-28.828
32.3572-0.12270.34131.660.33094.3334-0.0809-0.13850.20840.00350.0787-0.0178-0.03470.10340.00220.00610.0059-0.00120.015-0.010.02894.45528.08-16.102
46.1216-1.3822.76824.4824-1.40298.9257-0.0571-0.18310.0740.04870.08280.5532-0.2098-0.7521-0.02570.0369-0.01120.03340.0915-0.02620.1102-9.33725.3-16.702
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 374
2X-RAY DIFFRACTION1A2201
3X-RAY DIFFRACTION2A1055 - 1139
4X-RAY DIFFRACTION3A2032 - 2129
5X-RAY DIFFRACTION4B37 - 52
6X-RAY DIFFRACTION4B101

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