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- PDB-7f61: Crystal structure of human histamine receptor H3R in complex with... -

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Basic information

Entry
Database: PDB / ID: 7f61
TitleCrystal structure of human histamine receptor H3R in complex with antagonist PF03654746
Components
  • Histamine H3 receptor
  • Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / GPCR / histamine receptor
Function / homology
Function and homology information


Histamine receptors / histamine receptor activity / negative regulation of glutamate secretion / regulation of norepinephrine secretion / G protein-coupled acetylcholine receptor activity / negative regulation of serotonin secretion / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / neurotransmitter secretion / G protein-coupled serotonin receptor activity / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger ...Histamine receptors / histamine receptor activity / negative regulation of glutamate secretion / regulation of norepinephrine secretion / G protein-coupled acetylcholine receptor activity / negative regulation of serotonin secretion / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / neurotransmitter secretion / G protein-coupled serotonin receptor activity / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / electron transport chain / cognition / presynapse / chemical synaptic transmission / periplasmic space / electron transfer activity / iron ion binding / synapse / dendrite / heme binding / plasma membrane
Similarity search - Function
Histamine H3 receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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)
Similarity search - Domain/homology
Chem-1IB / CHOLESTEROL / Soluble cytochrome b562 / Histamine H3 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPeng, X. / Zhang, H.
Funding support China, 6items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0508100 China
National Natural Science Foundation of China (NSFC)81722044 China
National Natural Science Foundation of China (NSFC)91753115 China
National Natural Science Foundation of China (NSFC)21778049 China
National Natural Science Foundation of China (NSFC)81861148018 China
Ministry of Science and Technology (MoST, China)2018ZX09711002 China
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for recognition of antihistamine drug by human histamine receptor.
Authors: Peng, X. / Yang, L. / Liu, Z. / Lou, S. / Mei, S. / Li, M. / Chen, Z. / Zhang, H.
History
DepositionJun 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histamine H3 receptor
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5504
Polymers61,8412
Non-polymers7092
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint1 kcal/mol
Surface area20350 Å2
Unit cell
Length a, b, c (Å)71.124, 165.624, 42.651
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Histamine H3 receptor / H3R / HH3R / G-protein coupled receptor 97


Mass: 45009.184 Da / Num. of mol.: 1 / Mutation: S121K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRH3, GPCR97 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y5N1
#2: Protein Soluble cytochrome b562 / Cytochrome b-562


Mass: 16831.879 Da / Num. of mol.: 1 / Mutation: M7W, H102I, R106L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0ABE7
#3: Chemical ChemComp-1IB / N-ethyl-3-fluoranyl-3-[3-fluoranyl-4-(pyrrolidin-1-ylmethyl)phenyl]cyclobutane-1-carboxamide


Mass: 322.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24F2N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: antagonist*YM
#4: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 39.44 %
Crystal growTemperature: 294 K / Method: lipidic cubic phase
Details: 100mM sodium cacodylate trihydrate, pH6.4, 90mM sodium citrate, 34% PEG400, 2% Dichloromethane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 16071 / % possible obs: 98.5 % / Redundancy: 5.2 % / CC1/2: 0.982 / Rmerge(I) obs: 0.146 / Net I/σ(I): 6.78
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.61 / Num. unique obs: 1448 / CC1/2: 0.522

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4u15

4u15


Resolution: 2.6→29.896 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.864 / SU B: 0.6 / SU ML: 0 / Cross valid method: FREE R-VALUE / ESU R: 0.284 / ESU R Free: 0.353
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2846 788 4.931 %
Rwork0.229 15194 -
all0.232 --
obs-15194 98.405 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.717 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3255 0 51 8 3314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6670.314490.3051121X-RAY DIFFRACTION97.4188
2.667-2.7390.291460.31036X-RAY DIFFRACTION98.1851
2.739-2.8180.273550.2961029X-RAY DIFFRACTION97.0457
2.818-2.9040.304450.2651004X-RAY DIFFRACTION98.4053
2.904-2.9980.315500.263983X-RAY DIFFRACTION98.9464
2.998-3.1030.294550.235958X-RAY DIFFRACTION98.7329
3.103-3.2180.342530.237913X-RAY DIFFRACTION98.9754
3.218-3.3480.294490.208884X-RAY DIFFRACTION99.2553
3.348-3.4950.294490.19852X-RAY DIFFRACTION98.9023
3.495-3.6630.25400.196805X-RAY DIFFRACTION98.0278
3.663-3.8580.249350.194812X-RAY DIFFRACTION99.6471
3.858-4.0880.249380.204738X-RAY DIFFRACTION99.6149
4.088-4.3640.263430.224718X-RAY DIFFRACTION99.8688
4.364-4.7060.302280.225667X-RAY DIFFRACTION99.2857
4.706-5.1420.32400.234603X-RAY DIFFRACTION99.0755
5.142-5.7280.367310.253541X-RAY DIFFRACTION96.7851
5.728-6.5740.305250.259509X-RAY DIFFRACTION99.0724
6.574-7.9560.287310.19433X-RAY DIFFRACTION99.3576
7.956-100.141160.157344X-RAY DIFFRACTION94.4882
10.873-29.8960.26590.26242X-RAY DIFFRACTION98.8189

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