[English] 日本語
Yorodumi
- PDB-4rwf: Crystal structure of the CLR:RAMP2 extracellular domain heterodim... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Ethylene glycol


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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more