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- PDB-2ziy: Crystal structure of squid rhodopsin -

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Basic information

Entry
Database: PDB / ID: 2ziy
TitleCrystal structure of squid rhodopsin
ComponentsRhodopsin
KeywordsSIGNALING PROTEIN / transmembrane helices / Chromophore / G-protein coupled receptor / Glycoprotein / Lipoprotein / Palmitate / Phosphoprotein / Photoreceptor protein / Receptor / Retinal protein / Sensory transduction / Transducer / Vision
Function / homology
Function and homology information


rhabdomere membrane / G protein-coupled photoreceptor activity / cellular response to light stimulus / retinal binding / phototransduction / visual perception / membrane / plasma membrane
Similarity search - Function
XYPPX repeat / XYPPX repeat (two copies) / 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. ...XYPPX repeat / XYPPX repeat (two copies) / 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
PALMITIC ACID / RETINAL / Rhodopsin
Similarity search - Component
Biological speciesTodarodes pacificus (Japanese flying squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsMiyano, M. / Shimamura, T.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of squid rhodopsin with intracellularly extended cytoplasmic region
Authors: Shimamura, T. / Hiraki, K. / Takahashi, N. / Hori, T. / Ago, H. / Masuda, K. / Takio, K. / Ishiguro, M. / Miyano, M.
History
DepositionFeb 27, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6264
Polymers41,8291
Non-polymers7973
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Rhodopsin
hetero molecules

A: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2528
Polymers83,6572
Non-polymers1,5956
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5550 Å2
ΔGint-17.2 kcal/mol
Surface area36970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.319, 108.746, 142.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Rhodopsin


Mass: 41828.742 Da / Num. of mol.: 1
Fragment: Truncation of C-terminal polypro by V8-protease, UNP residues 2-373:VAL18ILE confirmed by MS
Source method: isolated from a natural source
Source: (natural) Todarodes pacificus (Japanese flying squid)
References: UniProt: P31356
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
Has protein modificationY
Sequence detailsTHERE IS CONFLICTS BETWEEN SEQRES(ILE A 17) AND SEQUENCE DATABASE (VAL). THE AUTHORS CONFIRMED ...THERE IS CONFLICTS BETWEEN SEQRES(ILE A 17) AND SEQUENCE DATABASE (VAL). THE AUTHORS CONFIRMED EXPERIMENTALLY BY N-TERMINAL AMINO ACID SEQUENCING, AND THE SEQRES IS CORRECT AND IS THE TRUE IDENTITY OF THIS RESIDUE AND IS NATURAL VARIANT.

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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: 3.9 Å3/Da / Density % sol: 68.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28% PEG400, 0.1M HEPES, 8% ethylene glycol, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.9795 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.7→43.2 Å / Num. all: 6680 / Num. obs: 6680 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.1
Reflection shellResolution: 3.7→3.83 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 1.3 / Num. unique all: 535 / % possible all: 74.3

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GZM

1gzm


Resolution: 3.7→43.2 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: The structure was refined also with REFMAC 5.0
RfactorNum. reflection% reflectionSelection details
Rfree0.33 725 -RANDOM
Rwork0.302 ---
obs-6647 93.3 %-
Refinement stepCycle: LAST / Resolution: 3.7→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 54 0 2980
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016981
X-RAY DIFFRACTIONc_angle_deg1.67163
LS refinement shellResolution: 3.7→3.87 Å
RfactorNum. reflection% reflection
Rfree0.432 64 -
Rwork0.4141 --
obs-572 74.3 %

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