[English] 日本語
Yorodumi
- PDB-5tud: Structural Insights into the Extracellular Recognition of the Hum... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tud
TitleStructural Insights into the Extracellular Recognition of the Human Serotonin 2B Receptor by an Antibody
Components
  • 5-hydroxytryptamine receptor 2B,Soluble cytochrome b562 chimera
  • Anti-5-HT2B Fab heavy chain
  • Anti-5-HT2B Fab light chain
KeywordsSIGNALING PROTEIN / 7-TM / GPCR / Fab / complex
Function / homology
Function and homology information


intestine smooth muscle contraction / Gq/11-coupled serotonin receptor activity / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / regulation of behavior / G protein-coupled serotonin receptor complex / Serotonin receptors / serotonin receptor activity / G protein-coupled serotonin receptor activity / phospholipase C-activating serotonin receptor signaling pathway ...intestine smooth muscle contraction / Gq/11-coupled serotonin receptor activity / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / regulation of behavior / G protein-coupled serotonin receptor complex / Serotonin receptors / serotonin receptor activity / G protein-coupled serotonin receptor activity / phospholipase C-activating serotonin receptor signaling pathway / serotonin receptor signaling pathway / embryonic morphogenesis / serotonin binding / neurotransmitter receptor activity / vasoconstriction / cardiac muscle hypertrophy / neural crest cell migration / neural crest cell differentiation / cGMP-mediated signaling / positive regulation of cell division / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / G-protein alpha-subunit binding / heart morphogenesis / positive regulation of endothelial cell proliferation / release of sequestered calcium ion into cytosol / ERK1 and ERK2 cascade / GTPase activator activity / positive regulation of cytokine production / calcium-mediated signaling / electron transport chain / intracellular calcium ion homeostasis / chemical synaptic transmission / G alpha (q) signalling events / positive regulation of canonical NF-kappaB signal transduction / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / G protein-coupled receptor signaling pathway / iron ion binding / response to xenobiotic stimulus / positive regulation of cell population proliferation / synapse / heme binding / dendrite / negative regulation of apoptotic process / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
5-Hydroxytryptamine 2B receptor / 5-hydroxytryptamine receptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. ...5-Hydroxytryptamine 2B receptor / 5-hydroxytryptamine receptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ergotamine / Soluble cytochrome b562 / 5-hydroxytryptamine receptor 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsIshchenko, A. / Wacker, D. / Kapoor, M. / Zhang, A. / Han, G.W. / Basu, S. / Boutet, S. / James, D. / Wang, D. / Weierstall, U. ...Ishchenko, A. / Wacker, D. / Kapoor, M. / Zhang, A. / Han, G.W. / Basu, S. / Boutet, S. / James, D. / Wang, D. / Weierstall, U. / Liu, W. / Katritch, V. / Stevens, R.C. / Cherezov, V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM108635 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094618 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural insights into the extracellular recognition of the human serotonin 2B receptor by an antibody.
Authors: Ishchenko, A. / Wacker, D. / Kapoor, M. / Zhang, A. / Han, G.W. / Basu, S. / Patel, N. / Messerschmidt, M. / Weierstall, U. / Liu, W. / Katritch, V. / Roth, B.L. / Stevens, R.C. / Cherezov, V.
History
DepositionNov 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 28, 2018Group: Data collection
Category: diffrn / pdbx_serial_crystallography_data_reduction ...diffrn / pdbx_serial_crystallography_data_reduction / pdbx_serial_crystallography_measurement / pdbx_serial_crystallography_sample_delivery / pdbx_serial_crystallography_sample_delivery_injection
Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 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
Revision 1.7Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5-hydroxytryptamine receptor 2B,Soluble cytochrome b562 chimera
B: Anti-5-HT2B Fab light chain
C: Anti-5-HT2B Fab heavy chain
D: 5-hydroxytryptamine receptor 2B,Soluble cytochrome b562 chimera
E: Anti-5-HT2B Fab light chain
F: Anti-5-HT2B Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,4288
Polymers200,2656
Non-polymers1,1632
Water00
1
A: 5-hydroxytryptamine receptor 2B,Soluble cytochrome b562 chimera
B: Anti-5-HT2B Fab light chain
C: Anti-5-HT2B Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7144
Polymers100,1323
Non-polymers5821
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-31 kcal/mol
Surface area38090 Å2
MethodPISA
2
D: 5-hydroxytryptamine receptor 2B,Soluble cytochrome b562 chimera
E: Anti-5-HT2B Fab light chain
F: Anti-5-HT2B Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7144
Polymers100,1323
Non-polymers5821
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-37 kcal/mol
Surface area37810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.290, 118.860, 145.380
Angle α, β, γ (deg.)90.00, 90.37, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein 5-hydroxytryptamine receptor 2B,Soluble cytochrome b562 chimera / 5-HT2B / Serotonin receptor 2B / Cytochrome b-562


Mass: 51497.035 Da / Num. of mol.: 2
Fragment: UNP P41595 residues 36-248 and 314-405 linked by UNP P0ABE7 residues 23-128
Mutation: M144W, M1007W, H1102I, R1106L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: HTR2B, cybC / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P41595, UniProt: P0ABE7
#2: Antibody Anti-5-HT2B Fab light chain


Mass: 23151.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Antibody Anti-5-HT2B Fab heavy chain


Mass: 25483.455 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Chemical ChemComp-ERM / Ergotamine


Mass: 581.661 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H35N5O5 / Comment: neurotransmitter, alkaloid*YM
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.7
Details: Tris/HCL pH 7.7, 60 mM Sodium/Potassium Tartrate, 25% PEG400.

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.56 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Jan 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.56 Å / Relative weight: 1
ReflectionResolution: 3→35.64 Å / Num. obs: 48606 / % possible obs: 100 % / Redundancy: 310.3 % / Biso Wilson estimate: 90.32 Å2 / Net I/σ(I): 4.3
Reflection shellResolution: 3→3.1 Å / Redundancy: 120.26 % / Mean I/σ(I) obs: 0.4 / CC1/2: 0.34 / % possible all: 100
Serial crystallography measurementPhotons per pulse: 390000000000 Tphotons/pulse / Pulse duration: 35 fsec. / Pulse photon energy: 7.95 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionInjector diameter: 1.5 µm
Serial crystallography data reductionFrames failed index: 193328 / Frames indexed: 52291 / Frames total: 1877040

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
CrystFELdata reduction
PHASERphasing
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NC3

4nc3


Resolution: 3→35.64 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.896 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.822 / SU Rfree Blow DPI: 0.357
Details: unmodeled densities (potentially Zn ion) near (1) His232, His235 of chain C & Asp1 of chain E, and (2) His233, His231 of Chain C & His1063 of chain A
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2259 4.65 %RANDOM
Rwork0.227 ---
obs0.228 48606 99.9 %-
Displacement parametersBiso mean: 106.1 Å2
Baniso -1Baniso -2Baniso -3
1-7.2629 Å20 Å22.1576 Å2
2---22.6624 Å20 Å2
3---15.3994 Å2
Refine analyzeLuzzati coordinate error obs: 0.62 Å
Refinement stepCycle: 1 / Resolution: 3→35.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12298 0 86 0 12384
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00512712HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7617399HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5649SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes239HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1910HARMONIC5
X-RAY DIFFRACTIONt_it12712HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.08
X-RAY DIFFRACTIONt_other_torsion2.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1776SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14866SEMIHARMONIC4
LS refinement shellResolution: 3→3.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 167 4.7 %
Rwork0.242 3388 -
all0.243 3555 -
obs--99.58 %
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)
10.1220.44761.08430.89881.5574.38920.1139-0.1398-0.11610.0925-0.0277-0.06510.3326-0.1177-0.0862-0.16450.0496-0.01390.20040.0639-0.195316.0121-29.485962.7126
21.12480.3938-0.20761.0764-1.39184.86410.1025-0.06490.03520.16650.11140.2283-0.1734-0.2297-0.2139-0.05120.00880.0208-0.07990.023-0.154920.4383-10.5337139.413
31.00440.363-1.40690.51-0.155.3519-0.03820.0285-0.0138-0.14680.18340.07290.458-0.5429-0.1452-0.035-0.0764-0.074-0.05560.0022-0.166618.0545-26.5149130.8453
40.01440.4516-1.12680.6978-1.34052.53940.1155-0.26840.09960.1445-0.1052-0.0632-0.37020.2745-0.0103-0.0947-0.0481-0.01750.26820.0301-0.176818.7411-64.038959.9866
51.42030.2840.90520.94520.45185.14890.162-0.052-0.01660.1574-0.1126-0.0160.1822-0.1227-0.0494-0.1409-0.04460.01670.0120.0111-0.216516.9535-86.1553135.8512
61.86730.22322.12020.38340.47944.9011-0.1281-0.01730.1042-0.11620.02990.0414-0.3728-0.38620.0982-0.07040.0344-0.0173-0.087-0.0025-0.12219.5503-69.5515128.7206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|54 - A|1106 }
2X-RAY DIFFRACTION2{ B|1 - B|211 }
3X-RAY DIFFRACTION3{ C|1 - C|235 }
4X-RAY DIFFRACTION4{ D|55 - D|1106 }
5X-RAY DIFFRACTION5{ E|1 - E|211 }
6X-RAY DIFFRACTION6{ F|1 - F|233 }

+
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