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- PDB-9fow: GPR180 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 9fow
TitleGPR180 N-terminal domain
ComponentsIntegral membrane protein GPR180
KeywordsUNKNOWN FUNCTION / GOLD / GOST / GPR180
Function / homology
Function and homology information


response to pheromone / G protein-coupled receptor signaling pathway / membrane
Similarity search - Function
Intimal thickness related receptor, IRP / : / : / GPR180/TMEM145, transmembrane domain / GP180, GOLD domain
Similarity search - Domain/homology
ACETATE ION / Integral membrane protein GPR180
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.878 Å
AuthorsMitrovic, S.A. / Reindl, S. / Nar, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2024
Title: GPR180 is a new member of the Golgi-dynamics domain seven-transmembrane helix protein family.
Authors: Mitrovic, S.A. / Demalgiriya-Gamage, C. / Winter, L.M. / Kiechle, T. / Ebenhoch, R. / Neubauer, H. / Stierstorfer, B. / Frego, L. / Wolfrum, C. / Reindl, S. / Nar, H.
History
DepositionJun 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integral membrane protein GPR180
B: Integral membrane protein GPR180
C: Integral membrane protein GPR180
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,37113
Polymers49,0083
Non-polymers2,36210
Water2,072115
1
A: Integral membrane protein GPR180
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7084
Polymers16,3361
Non-polymers3723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Integral membrane protein GPR180
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3556
Polymers16,3361
Non-polymers1,0195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Integral membrane protein GPR180
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3073
Polymers16,3361
Non-polymers9712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.116, 143.116, 43.556
Angle α, β, γ (deg.)90, 90, 120
Int Tables number172
Space group name H-MP64

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Integral membrane protein GPR180


Mass: 16336.132 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gpr180, MNCb-3029 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8BPS4

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Sugars , 3 types, 3 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1-2/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 878.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3-2/a3-b1_a4-c1_a6-e1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 122 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.93 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20% glycerol, 16% PEG 8K, 0.04M kaliumdihydrogenphosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000036 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000036 Å / Relative weight: 1
ReflectionResolution: 1.878→123.942 Å / Num. obs: 37931 / % possible obs: 90.3 % / Redundancy: 18.6 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 18.8
Reflection shellResolution: 1.878→1.974 Å / Redundancy: 20.8 % / Rmerge(I) obs: 2.601 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 37873 / Rsym value: 2.601 / % possible all: 32.9

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
XDSFeb 5, 2021data reduction
autoPROC1.1.7data scaling
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.878→25.25 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.229 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.157 / SU Rfree Blow DPI: 0.135 / SU Rfree Cruickshank DPI: 0.137
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 1816 -RANDOM
Rwork0.221 ---
obs0.2217 37910 90.3 %-
Displacement parametersBiso mean: 53.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.3219 Å20 Å20 Å2
2--0.3219 Å20 Å2
3----0.6439 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.878→25.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3088 0 157 115 3360
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086482HARMONIC2
X-RAY DIFFRACTIONt_angle_deg111649HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1975SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1036HARMONIC5
X-RAY DIFFRACTIONt_it6480HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion456SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact5384SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.59
X-RAY DIFFRACTIONt_other_torsion14.19
LS refinement shellResolution: 1.88→1.94 Å
RfactorNum. reflection% reflection
Rfree0.3027 38 -
Rwork0.2807 --
obs0.2819 759 19.39 %
Refinement TLS params.

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)
10.77720.253-0.23743.308-0.09770.74780.10420.006-0.02170.006-0.15060.0408-0.02170.04080.0464-0.0632-0.0203-0.0322-0.04380.02290.048748.1927-53.9025-6.7724
22.67570.35450.35781.11890.09861.17420.05570.04630.19320.0463-0.055-0.05160.1932-0.0516-0.0007-0.0169-0.01610.00030.0117-0.008-0.076566.9648-72.4129-5.1529
31.40941.3003-0.86771.6829-1.35193.2997-0.2161-0.28360.6921-0.28360.02260.0410.69210.0410.19360.06830.03310.05490.0056-0.0451-0.094276.4423-82.1256-20.0505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A23 - 154
2X-RAY DIFFRACTION1{ A|* }A201 - 212
3X-RAY DIFFRACTION2{ B|* }B23 - 168
4X-RAY DIFFRACTION2{ B|* }B201 - 208
5X-RAY DIFFRACTION3{ C|* }C24 - 166
6X-RAY DIFFRACTION3{ C|* }C201 - 208

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