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- PDB-1gzm: Structure of Bovine Rhodopsin in a Trigonal Crystal Form -

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Basic information

Entry
Database: PDB / ID: 1gzm
TitleStructure of Bovine Rhodopsin in a Trigonal Crystal Form
ComponentsRHODOPSIN
KeywordsSIGNALING PROTEIN / PHOTORECEPTOR / RETINAL PROTEIN / VISUAL PIGMENT / G-PROTEIN COUPLED RECEPTOR / INTEGRAL MEMBRANE PROTEIN / PALMITATE / PHOSPHORYLATION
Function / homology
Function and homology information


Opsins / VxPx cargo-targeting to cilium / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / podosome assembly / 11-cis retinal binding ...Opsins / VxPx cargo-targeting to cilium / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / podosome assembly / 11-cis retinal binding / G protein-coupled photoreceptor activity / photoreceptor inner segment membrane / rod photoreceptor outer segment / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / thermotaxis / Activation of the phototransduction cascade / outer membrane / detection of temperature stimulus involved in thermoception / response to light intensity / photoreceptor cell maintenance / arrestin family protein binding / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction, visible light / G-protein alpha-subunit binding / phototransduction / photoreceptor outer segment / sperm midpiece / visual perception / guanyl-nucleotide exchange factor activity / microtubule cytoskeleton organization / photoreceptor disc membrane / cell-cell junction / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / zinc ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx ...Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / PALMITIC ACID / RETINAL / Rhodopsin
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLi, J.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Structure of Bovine Rhodopsin in a Trigonal Crystal Form
Authors: Li, J. / Edwards, P. / Burghammer, M. / Villa, C. / Schertler, G.F.X.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Crystals of Native and Modified Bovine Rhodopsins and Their Heavy Atom Derivatives
Authors: Edwards, P. / Li, J. / Burghammer, M. / Mcdowell, J.H. / Villa, C. / Hargrave, P.A. / Schertler, G.F.X.
History
DepositionMay 24, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 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
A: RHODOPSIN
B: RHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,93631
Polymers78,1152
Non-polymers9,82129
Water72140
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-37 kcal/mol
Surface area35620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.820, 103.820, 76.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, -0.00056, 0.00019), (0.00056, -1, -0.0003), (0.00019, -0.0003, 1)51.91986, 29.94182, 0.00307
2given(-1, -0.00056, 0.00019), (0.00056, -1, -0.0003), (0.00019, -0.0003, 1)51.91986, 29.94182, 0.00307
3given(-0.99999, -0.00308, 0.00187), (0.00309, -0.99999, 0.00094), (0.00186, 0.00095, 1)52.03257, 29.86744, -0.09026

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Components

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Protein / Sugars , 2 types, 6 molecules AB

#1: Protein RHODOPSIN


Mass: 39057.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: DISULFIDE LINK BETWEEN A110 AND A187, AND B110 AND B187
Source: (natural) BOS TAURUS (domestic cattle) / Cell: ROD PHOTORECEPTOR / Organ: EYE / Tissue: RETINA / References: UniProt: P02699
#2: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 7 types, 65 molecules

#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#4: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#6: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#7: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsLIGHT-ABSORBING MOLECULES THAT MEDIATE VISION. CONSIST OF AN APOPROTEIN, OPSIN, COVALENTLY BOUND TO ...LIGHT-ABSORBING MOLECULES THAT MEDIATE VISION. CONSIST OF AN APOPROTEIN, OPSIN, COVALENTLY BOUND TO 11-CIS-RETINAL.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 49 %
Description: DATA WERE COLLECTED USING MICROFOCUSED SYNCHROTRON SOURCE.
Crystal growMethod: vapor diffusion, sitting drop / pH: 8.5
Details: VAPOUR DIFFUSION IN SITTING DROPS OF 15 MG/ML PROTEIN AND 0.2% C8E4, 0.05%LDAO AGAINST 0.8M LI2SO4, 1.6% PEG8000 AND 20% GLYCEROL, pH 8.5
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, sitting drop / Details: Edwards, P., (2004) J. Mol. Biol., 343, 1439.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
20.6-1.1 M1reservoirLi2SO4
31.6 %PEG80001reservoir
420 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.782
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.782 Å / Relative weight: 1
ReflectionResolution: 2.65→46 Å / Num. obs: 26026 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 58.2 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 11
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 1.4 / % possible all: 86
Reflection
*PLUS
% possible obs: 97 %
Reflection shell
*PLUS
% possible obs: 86.1 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F88

1f88


Resolution: 2.65→46 Å / Rfactor Rfree error: 0.0066 / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE FOLLOWING HOH RESIDUES ARE EQUIVALENT BY NON- CRYSTALLOGRAPHIC SYMMETRY AND ARE EQUIVALENT TO THESE RESIDUES IN THE PRIMARY REFERENCE: U1 == V1, AND WATER RESIDUE 7 IN REFERENCE U2 == ...Details: THE FOLLOWING HOH RESIDUES ARE EQUIVALENT BY NON- CRYSTALLOGRAPHIC SYMMETRY AND ARE EQUIVALENT TO THESE RESIDUES IN THE PRIMARY REFERENCE: U1 == V1, AND WATER RESIDUE 7 IN REFERENCE U2 == V3, AND WATER RESIDUE 16 IN REFERENCE U3 == V4, AND WATER RESIDUE 8 IN REFERENCE U4 == V5, AND WATER RESIDUE 11 IN REFERENCE U5 == V6, AND WATER RESIDUE 4 IN REFERENCE U6 == V7, AND WATER RESIDUE 13 IN REFERENCE U7 == V11, AND WATER RESIDUE 6 IN REFERENCE U8 == V9, AND WATER RESIDUE 3 IN REFERENCE U9 == V19, AND WATER RESIDUE 15 IN REFERENCE U10 == V3, AND WATER RESIDUE 18 IN REFERENCE U11 == V13, AND WATER RESIDUE 5 IN REFERENCE U12 == V14, AND WATER RESIDUE 14 IN REFERENCE U13 == V15, AND WATER RESIDUE 19 IN REFERENCE U14 == V16, AND WATER RESIDUE 9 IN REFERENCE U15 == V17, AND WATER RESIDUE 1 IN REFERENCE U16 == V12, AND WATER RESIDUE 17 IN REFERENCE U17 == V18, AND WATER RESIDUE 20 IN REFERENCE U18 == V2, AND WATER RESIDUE 12 IN REFERENCE U19 == V19, AND WATER RESIDUE 2 IN REFERENCE U20 == V20, AND WATER RESIDUE 10 IN REFERENCE THE FOLLOWING CARBOHYDRATE RESIDUES ARE EQUIVALENT BY NON- CRYSTALLOGRAPHIC SYMMETRY: A1335 IS EQUIVALENT TO B1335 A1336 IS EQUIVALENT TO B1336 A1337 IS EQUIVALENT TO B1350 A1338 IS EQUIVALENT TO B1337 A1339 IS EQUIVALENT TO B1338 A1340 IS EQUIVALENT TO B1339
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 1322 4.9 %RANDOM
Rwork0.2015 ---
obs0.2015 24704 97 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 56 Å2
Baniso -1Baniso -2Baniso -3
1--4.454 Å2-8.526 Å20 Å2
2---4.454 Å20 Å2
3---8.907 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.65→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 540 40 5792
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.781.5
X-RAY DIFFRACTIONc_mcangle_it3.132.5
X-RAY DIFFRACTIONc_scbond_it2.392
X-RAY DIFFRACTIONc_scangle_it3.813
Refine LS restraints NCSRms dev Biso : 1 Å2 / Rms dev position: 0.515 Å / Weight position: 5
LS refinement shellResolution: 2.65→2.74 Å / Rfactor Rfree error: 0.0275 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3146 130 4.8 %
Rwork0.3089 2165 -
obs--84.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_LYR7_CYP.PARAMPROTEIN_LYR2_CYP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4LIPID-DETG3.PARAMLIPID-DETG.TOP
Refinement
*PLUS
Lowest resolution: 46 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.293
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.876
LS refinement shell
*PLUS
Rfactor Rfree: 0.315 / Rfactor Rwork: 0.312

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