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- PDB-3rze: Structure of the human histamine H1 receptor in complex with doxepin -

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Basic information

Entry
Database: PDB / ID: 3rze
TitleStructure of the human histamine H1 receptor in complex with doxepin
ComponentsHistamine H1 receptor, Lysozyme chimera
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Membrane Protein / GPCR Network / GPCR
Function / homology
Function and homology information


Histamine receptors / histamine receptor activity / regulation of vascular permeability / cellular response to histamine / G protein-coupled serotonin receptor activity / neurotransmitter receptor activity / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / positive regulation of vasoconstriction / viral release from host cell by cytolysis / peptidoglycan catabolic process ...Histamine receptors / histamine receptor activity / regulation of vascular permeability / cellular response to histamine / G protein-coupled serotonin receptor activity / neurotransmitter receptor activity / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / positive regulation of vasoconstriction / viral release from host cell by cytolysis / peptidoglycan catabolic process / regulation of synaptic plasticity / visual learning / memory / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / phospholipase C-activating G protein-coupled receptor signaling pathway / chemical synaptic transmission / G alpha (q) signalling events / host cell cytoplasm / defense response to bacterium / inflammatory response / G protein-coupled receptor signaling pathway / dendrite / synapse / plasma membrane / cytosol
Similarity search - Function
Histamine H1 receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx ...Histamine H1 receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme / 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) / Lysozyme-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-5EH / Chem-D7V / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / Endolysin / Histamine H1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsShimamura, T. / Han, G.W. / Shiroishi, M. / Weyand, S. / Tsujimoto, H. / Winter, G. / Katritch, V. / Abagyan, R. / Cherezov, V. / Liu, W. ...Shimamura, T. / Han, G.W. / Shiroishi, M. / Weyand, S. / Tsujimoto, H. / Winter, G. / Katritch, V. / Abagyan, R. / Cherezov, V. / Liu, W. / Kobayashi, T. / Stevens, R. / Iwata, S. / GPCR Network (GPCR)
CitationJournal: Nature / Year: 2011
Title: Structure of the human histamine H1 receptor complex with doxepin.
Authors: Shimamura, T. / Shiroishi, M. / Weyand, S. / Tsujimoto, H. / Winter, G. / Katritch, V. / Abagyan, R. / Cherezov, V. / Liu, W. / Han, G.W. / Kobayashi, T. / Stevens, R.C. / Iwata, S.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author
Revision 1.5Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histamine H1 receptor, Lysozyme chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5837
Polymers52,3831
Non-polymers1,2006
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.144, 88.144, 331.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histamine H1 receptor, Lysozyme chimera / H1R / HH1R / Endolysin / Lysis protein / Muramidase


Mass: 52382.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: HRH1, E / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1163 / References: UniProt: P35367, UniProt: P00720, lysozyme

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Non-polymers , 5 types, 8 molecules

#2: Chemical ChemComp-5EH / (3E)-3-(dibenzo[b,e]oxepin-11(6H)-ylidene)-N,N-dimethylpropan-1-amine / Doxepin


Mass: 279.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21NO / Comment: medication, antidepressant*YM
#3: Chemical ChemComp-D7V / (3Z)-3-(dibenzo[b,e]oxepin-11(6H)-ylidene)-N,N-dimethylpropan-1-amine / Cidoxepin


Mass: 279.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21NO / Comment: antidepressant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE PROTEIN IS A FUSION PROTEIN WITH RESIDUES ASN1002-TYR1161 OF T4 LYSOZYME INSERTED BETWEEN ...THE PROTEIN IS A FUSION PROTEIN WITH RESIDUES ASN1002-TYR1161 OF T4 LYSOZYME INSERTED BETWEEN CYS221 AND LEU450 OF H1.

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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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 293 K / pH: 4.5
Details: 26-30% PEG400, 300mM ammonium phosphate, 10mM MgCl2, 100mM Na-citrate pH 4.5, 1mM doxepin, Lipidic cubic phase, 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2010
RadiationMonochromator: ACCEL Fixed Exit Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3.1→34.5 Å / Num. all: 12152 / Num. obs: 12152 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 69.12 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.2
Reflection shellResolution: 3.1→3.4 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RH1

2rh1


Resolution: 3.1→34.5 Å / Cor.coef. Fo:Fc: 0.8823 / Cor.coef. Fo:Fc free: 0.8616 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 797 6.64 %RANDOM
Rwork0.2145 ---
obs0.217 11996 --
all-12152 --
Displacement parametersBiso mean: 89.19 Å2
Baniso -1Baniso -2Baniso -3
1--8.1276 Å20 Å20 Å2
2---8.1276 Å20 Å2
3---16.2553 Å2
Refine analyzeLuzzati coordinate error obs: 0.625 Å
Refinement stepCycle: LAST / Resolution: 3.1→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3481 0 72 2 3555
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013640HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.214934HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1232SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes62HARMONIC2
X-RAY DIFFRACTIONt_gen_planes522HARMONIC5
X-RAY DIFFRACTIONt_it3580HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion22.77
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion471SEMIHARMONIC5
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_contact4168SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.4 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2706 198 6.99 %
Rwork0.2343 2636 -
all0.2369 2834 -
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)
11.47-0.24570.64120.6106-0.69455.23070.1370.27840.0552-0.39490.0854-0.18550.1989-0.5442-0.22230.23240.0062-0.06540.09440.1063-0.30414.133433.539830.6388
22.86132.0242-0.44961.6343-0.28411.3082-0.17230.1254-0.256-0.28810.0967-0.22620.2478-0.01640.0756-0.10150.00060.0152-0.2329-0.0250.07135.967117.031870.5261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|28 - A|485 }A28 - 485
2X-RAY DIFFRACTION2{ A|1002 - A|1161 }A1002 - 1161

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