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- PDB-4iaq: Crystal structure of the chimeric protein of 5-HT1B-BRIL in compl... -

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Basic information

Entry
Database: PDB / ID: 4iaq
TitleCrystal structure of the chimeric protein of 5-HT1B-BRIL in complex with dihydroergotamine (PSI Community Target)
ComponentsChimera protein of human 5-hydroxytryptamine receptor 1B and E. Coli soluble cytochrome b562
KeywordsSignaling Protein / Electron Transport / dihydroergotamine / Novel protein engineering / GPCR Network / Membrane protein / PSI-Biology / Structural Genomics / GPCR / GPCR Dock
Function / homology
Function and homology information


voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / negative regulation of gamma-aminobutyric acid secretion / serotonergic synapse / G protein-coupled serotonin receptor complex / adenylate cyclase-inhibiting serotonin receptor signaling pathway / regulation of behavior / negative regulation of synaptic transmission, GABAergic / response to mineralocorticoid / negative regulation of serotonin secretion / Serotonin receptors ...voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / negative regulation of gamma-aminobutyric acid secretion / serotonergic synapse / G protein-coupled serotonin receptor complex / adenylate cyclase-inhibiting serotonin receptor signaling pathway / regulation of behavior / negative regulation of synaptic transmission, GABAergic / response to mineralocorticoid / negative regulation of serotonin secretion / Serotonin receptors / drinking behavior / cellular response to temperature stimulus / serotonin binding / bone remodeling / negative regulation of synaptic transmission, glutamatergic / vasoconstriction / G protein-coupled receptor internalization / G protein-coupled serotonin receptor activity / : / neurotransmitter receptor activity / regulation of synaptic vesicle exocytosis / cellular response to alkaloid / regulation of dopamine secretion / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / calyx of Held / positive regulation of vascular associated smooth muscle cell proliferation / presynaptic modulation of chemical synaptic transmission / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / response to cocaine / electron transport chain / cellular response to xenobiotic stimulus / presynaptic membrane / G alpha (i) signalling events / chemical synaptic transmission / response to ethanol / periplasmic space / electron transfer activity / iron ion binding / dendrite / heme binding / endoplasmic reticulum / plasma membrane
Similarity search - Function
5-Hydroxytryptamine 1B receptor / 5-hydroxytryptamine receptor family / Cytochrome c/b562 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Serpentine type 7TM GPCR chemoreceptor Srsx ...5-Hydroxytryptamine 1B receptor / 5-hydroxytryptamine receptor family / Cytochrome c/b562 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Dihydroergotamine / Soluble cytochrome b562 / 5-hydroxytryptamine receptor 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWang, C. / Jiang, Y. / Ma, J. / Wu, H. / Wacker, D. / Katritch, V. / Han, G.W. / Liu, W. / Huang, X. / Vardy, E. ...Wang, C. / Jiang, Y. / Ma, J. / Wu, H. / Wacker, D. / Katritch, V. / Han, G.W. / Liu, W. / Huang, X. / Vardy, E. / McCorvy, J.D. / Gao, X. / Zhou, E.X. / Melcher, K. / Zhang, C. / Bai, F. / Yang, H. / Yang, L. / Jiang, H. / Roth, B.L. / Cherezov, V. / Stevens, R.C. / Xu, H.E. / GPCR Network (GPCR)
CitationJournal: Science / Year: 2013
Title: Structural basis for molecular recognition at serotonin receptors.
Authors: Wang, C. / Jiang, Y. / Ma, J. / Wu, H. / Wacker, D. / Katritch, V. / Han, G.W. / Liu, W. / Huang, X.P. / Vardy, E. / McCorvy, J.D. / Gao, X. / Zhou, X.E. / Melcher, K. / Zhang, C. / Bai, F. ...Authors: Wang, C. / Jiang, Y. / Ma, J. / Wu, H. / Wacker, D. / Katritch, V. / Han, G.W. / Liu, W. / Huang, X.P. / Vardy, E. / McCorvy, J.D. / Gao, X. / Zhou, X.E. / Melcher, K. / Zhang, C. / Bai, F. / Yang, H. / Yang, L. / Jiang, H. / Roth, B.L. / Cherezov, V. / Stevens, R.C. / Xu, H.E.
History
DepositionDec 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2May 15, 2013Group: Database references
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chimera protein of human 5-hydroxytryptamine receptor 1B and E. Coli soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1012
Polymers45,5171
Non-polymers5841
Water905
1
A: Chimera protein of human 5-hydroxytryptamine receptor 1B and E. Coli soluble cytochrome b562
hetero molecules

A: Chimera protein of human 5-hydroxytryptamine receptor 1B and E. Coli soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2014
Polymers91,0342
Non-polymers1,1672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area1980 Å2
ΔGint-28 kcal/mol
Surface area36360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.740, 192.579, 74.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Chimera protein of human 5-hydroxytryptamine receptor 1B and E. Coli soluble cytochrome b562 / 5-HT-1B / 5-HT1B / S12 / Serotonin 1D beta receptor / 5-HT-1D-beta / Serotonin receptor 1B


Mass: 45517.031 Da / Num. of mol.: 1 / Mutation: L138W, M29W, H124I, R128L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: 5HT1B_HUMAN, HTR1B, HTR1DB, cybC / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P28222, UniProt: P0ABE7
#2: Chemical ChemComp-2GM / Dihydroergotamine


Mass: 583.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H37N5O5 / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 56

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.08 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8.7
Details: 100 mM Tris pH 8.7, 32-36% (v/v) PEG400, 90 mM sodium citrate tribasic dihydrate, 120 mM ammonium sulfate , Lipid Cubic Phase (LCP), temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.033
SYNCHROTRONAPS 21-ID-D21.033
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDAug 1, 2012mirrors
MARMOSAIC 300 mm CCD2CCDAug 1, 2012mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystalSINGLE WAVELENGTHMx-ray1
2double crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 14244 / % possible obs: 92.8 % / Redundancy: 11.1 % / Biso Wilson estimate: 79.31 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 24.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.4 / % possible all: 72.9

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
REFMACrefinement
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EIY

4eiy


Resolution: 2.8→35.06 Å / Cor.coef. Fo:Fc: 0.9159 / Cor.coef. Fo:Fc free: 0.8941 / SU R Cruickshank DPI: 0.873 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 647 4.98 %RANDOM
Rwork0.2364 ---
obs0.2374 12993 84.42 %-
Displacement parametersBiso mean: 97.29 Å2
Baniso -1Baniso -2Baniso -3
1-12.6669 Å20 Å20 Å2
2--0.0641 Å20 Å2
3----12.731 Å2
Refine analyzeLuzzati coordinate error obs: 0.578 Å
Refinement stepCycle: LAST / Resolution: 2.8→35.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2752 0 43 5 2800
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012869HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.093948HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1227SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes421HARMONIC5
X-RAY DIFFRACTIONt_it2869HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion3.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion415SEMIHARMONIC5
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_contact3541SEMIHARMONIC4
LS refinement shellResolution: 2.8→3.02 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2858 60 4.61 %
Rwork0.2566 1242 -
all0.2579 1302 -
obs--84.42 %
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)
10.8862-0.17590.12463.0338-0.40224.8226-0.126-0.0613-0.1410.1702-0.071-0.0915-0.1182-0.18360.1970.3862-0.0442-0.0497-0.1934-0.0149-0.3437-21.5753-3.638319.2809
23.98330.4063-3.8597.42350.67679.3765-0.005-0.2546-0.7722-0.1783-0.11320.50020.39991.08850.1182-0.16810.227-0.21310.0899-0.10210.3062-7.1107-46.386929.0148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|38 - A|387 }A38 - 387
2X-RAY DIFFRACTION2{ A|1001- A|1106 }A1001 - 1106

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