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- PDB-7c61: Crystal structure of 5-HT1B-BRIL and SRP2070_Fab complex -

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Basic information

Entry
Database: PDB / ID: 7c61
TitleCrystal structure of 5-HT1B-BRIL and SRP2070_Fab complex
Components
  • 5-hydroxytryptamine receptor 1B,Soluble cytochrome b562,5-hydroxytryptamine receptor 1B
  • IGG HEAVY CHAIN
  • IGG LIGHT CHAIN
KeywordsSIGNALING PROTEIN / GPCR / BRIL / Crystallization / Antibody
Function / homology
Function and homology information


negative regulation of serotonin secretion / serotonergic synapse / Gi/o-coupled serotonin receptor activity / G protein-coupled serotonin receptor complex / regulation of behavior / phospholipase C-activating serotonin receptor signaling pathway / Serotonin receptors / serotonin receptor activity / G protein-coupled serotonin receptor activity / vasoconstriction ...negative regulation of serotonin secretion / serotonergic synapse / Gi/o-coupled serotonin receptor activity / G protein-coupled serotonin receptor complex / regulation of behavior / phospholipase C-activating serotonin receptor signaling pathway / Serotonin receptors / serotonin receptor activity / G protein-coupled serotonin receptor activity / vasoconstriction / neurotransmitter receptor activity / bone remodeling / serotonin binding / cellular response to alkaloid / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / positive regulation of vascular associated smooth muscle cell proliferation / adenylate cyclase-inhibiting serotonin receptor signaling pathway / electron transport chain / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cellular response to xenobiotic stimulus / presynaptic membrane / G alpha (i) signalling events / chemical synaptic transmission / electron transfer activity / periplasmic space / iron ion binding / heme binding / dendrite / endoplasmic reticulum / plasma membrane
Similarity search - Function
5-Hydroxytryptamine 1B receptor / 5-hydroxytryptamine receptor family / Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) ...5-Hydroxytryptamine 1B receptor / 5-hydroxytryptamine receptor family / Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Ergotamine / Soluble cytochrome b562 / 5-hydroxytryptamine receptor 1B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsSuzuki, M. / Miyagi, H. / Asada, H. / Yasunaga, M. / Suno, C. / Takahashi, Y. / Saito, J. / Iwata, S.
CitationJournal: Sci Rep / Year: 2020
Title: The discovery of a new antibody for BRIL-fused GPCR structure determination.
Authors: Miyagi, H. / Asada, H. / Suzuki, M. / Takahashi, Y. / Yasunaga, M. / Suno, C. / Iwata, S. / Saito, J.I.
History
DepositionMay 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG LIGHT CHAIN
H: IGG HEAVY CHAIN
A: 5-hydroxytryptamine receptor 1B,Soluble cytochrome b562,5-hydroxytryptamine receptor 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6154
Polymers104,0333
Non-polymers5821
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)248.800, 65.700, 79.730
Angle α, β, γ (deg.)90.000, 98.790, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody IGG LIGHT CHAIN


Mass: 23681.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody IGG HEAVY CHAIN


Mass: 35237.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Protein 5-hydroxytryptamine receptor 1B,Soluble cytochrome b562,5-hydroxytryptamine receptor 1B / 5-HT1B / S12 / Serotonin 1D beta receptor / 5-HT-1D-beta / Serotonin receptor 1B / Cytochrome b-562 ...5-HT1B / S12 / Serotonin 1D beta receptor / 5-HT-1D-beta / Serotonin receptor 1B / Cytochrome b-562 / 5-HT1B / S12 / Serotonin 1D beta receptor / 5-HT-1D-beta / Serotonin receptor 1B


Mass: 45114.523 Da / Num. of mol.: 1 / Mutation: L138W,M1007W,H1102I,R1106L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: HTR1B, HTR1DB, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28222, UniProt: P0ABE7
#4: Chemical ChemComp-ERM / Ergotamine


Mass: 581.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H35N5O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotransmitter, alkaloid*YM
Has ligand of interestY
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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 30% PEG400, 0.4M SODIUM THIOCYANATE, 0.1M SODIUM ACETATE PH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→48.5 Å / Num. obs: 25815 / % possible obs: 100 % / Redundancy: 29.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.483 / Rpim(I) all: 0.09 / Rrim(I) all: 0.491 / Net I/σ(I): 9.2 / Num. measured all: 760396 / Scaling rejects: 271
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.1828.23.25711623441190.5940.6173.3171.6100
9-48.528.30.1072868710150.9920.0210.1093199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.02 Å48.5 Å
Translation7.02 Å48.5 Å

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHASER2.6.1phasing
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IAR

4iar


Resolution: 3→40 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.862 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2898 1247 4.8 %RANDOM
Rwork0.2522 ---
obs0.2541 24564 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 360.78 Å2 / Biso mean: 152.781 Å2 / Biso min: 42.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20.19 Å2
2--2.07 Å20 Å2
3----0.89 Å2
Refinement stepCycle: final / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6143 0 43 0 6186
Biso mean--287.77 --
Num. residues----790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136351
X-RAY DIFFRACTIONr_bond_other_d0.0360.0175754
X-RAY DIFFRACTIONr_angle_refined_deg1.681.6488676
X-RAY DIFFRACTIONr_angle_other_deg2.4131.57413345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2225781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78722.825269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.45515997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3961522
X-RAY DIFFRACTIONr_chiral_restr0.0670.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026980
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021339
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 79 -
Rwork0.34 1788 -
all-1867 -
obs--100 %
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)
11.04580.5316-0.2524.8483-0.10762.32420.0918-0.0209-0.109-0.3741-0.2755-0.2005-0.1322-0.00940.18370.27670.03530.03520.01650.01480.173249.20911.261101.632
21.076-0.2071-0.52385.8221-0.45422.6103-0.08360.0751-0.2495-0.4226-0.1105-0.5782-0.01810.81740.19410.58730.04480.21860.32890.02930.519770.39710.1275.091
30.7720.71270.87711.16910.7911.80150.08040.5525-0.1904-0.45960.0538-0.02150.2843-0.1254-0.13410.83740.0888-0.0291.9889-0.08021.8028-12.66-3.729101.64
46.8186-0.5119-1.23045.5728-1.3175.31250.01870.7790.06480.1018-0.13830.8716-0.1651-0.79110.11960.3993-0.00790.08180.1957-0.02260.353332.2166.203120.396
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 109
2X-RAY DIFFRACTION1H1 - 119
3X-RAY DIFFRACTION2L110 - 213
4X-RAY DIFFRACTION2H120 - 219
5X-RAY DIFFRACTION3A38 - 239
6X-RAY DIFFRACTION3A240 - 422

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