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- PDB-6fd8: Gamma-s crystallin dimer -

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Basic information

Entry
Database: PDB / ID: 6fd8
TitleGamma-s crystallin dimer
ComponentsBeta-crystallin S
KeywordsSTRUCTURAL PROTEIN / Crystallin / eye lens / vision / cataract.
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception / morphogenesis of an epithelium
Similarity search - Function
Crystallins / Gamma-B Crystallin; domain 1 / Beta/Gamma crystallin / : / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMabbitt, P.D. / Thorn, D.C. / Jackson, C.J. / Carver, J.A.
CitationJournal: J Mol Biol / Year: 2019
Title: The Structure and Stability of the Disulfide-Linked γS-Crystallin Dimer Provide Insight into Oxidation Products Associated with Lens Cataract Formation.
Authors: David C Thorn / Aidan B Grosas / Peter D Mabbitt / Nicholas J Ray / Colin J Jackson / John A Carver /
Abstract: The reducing environment in the eye lens diminishes with age, leading to significant oxidative stress. Oxidation of lens crystallin proteins is the major contributor to their destabilization and ...The reducing environment in the eye lens diminishes with age, leading to significant oxidative stress. Oxidation of lens crystallin proteins is the major contributor to their destabilization and deleterious aggregation that scatters visible light, obscures vision, and ultimately leads to cataract. However, the molecular basis for oxidation-induced aggregation is unknown. Using X-ray crystallography and small-angle X-ray scattering, we describe the structure of a disulfide-linked dimer of human γS-crystallin that was obtained via oxidation of C24. The γS-crystallin dimer is stable at glutathione concentrations comparable to those in aged and cataractous lenses. Moreover, dimerization of γS-crystallin significantly increases the protein's propensity to form large insoluble aggregates owing to non-cooperative domain unfolding, as is observed in crystallin variants associated with early-onset cataract. These findings provide insight into how oxidative modification of crystallins contributes to cataract and imply that early-onset and age-related forms of the disease share comparable development pathways.
History
DepositionDec 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.2Feb 6, 2019Group: Data collection / Database references / Derived calculations
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-crystallin S
B: Beta-crystallin S


Theoretical massNumber of molelcules
Total (without water)42,0682
Polymers42,0682
Non-polymers00
Water2,288127
1
A: Beta-crystallin S

B: Beta-crystallin S


Theoretical massNumber of molelcules
Total (without water)42,0682
Polymers42,0682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Unit cell
Length a, b, c (Å)49.632, 52.365, 53.972
Angle α, β, γ (deg.)108.72, 111.46, 105.50
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Beta-crystallin S / Gamma-S-crystallin / Gamma-crystallin S


Mass: 21033.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGS, CRYG8 / Production host: Escherichia coli (E. coli) / References: UniProt: P22914
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium tartrate dibasic dihydrate (pH 7.3), 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→43.114 Å / Num. obs: 23548 / % possible obs: 93.6 % / Redundancy: 2.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.022 / Net I/σ(I): 7.8
Reflection shellResolution: 2.1→2.2107 Å / Num. unique obs: 2372 / % possible all: 94.35

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VH1

5vh1


Resolution: 2.1→43.114 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 35.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2731 1044 4.46 %
Rwork0.226 --
obs0.2283 23387 92.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→43.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 0 127 3019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082978
X-RAY DIFFRACTIONf_angle_d0.9434018
X-RAY DIFFRACTIONf_dihedral_angle_d3.1741752
X-RAY DIFFRACTIONf_chiral_restr0.059384
X-RAY DIFFRACTIONf_plane_restr0.006526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.21070.38571300.32133218X-RAY DIFFRACTION94
2.2107-2.34920.4143960.37463088X-RAY DIFFRACTION88
2.3492-2.53060.37761670.28843193X-RAY DIFFRACTION94
2.5306-2.78520.33241600.27843225X-RAY DIFFRACTION94
2.7852-3.18820.2989900.24163307X-RAY DIFFRACTION95
3.1882-4.01630.27421400.19573135X-RAY DIFFRACTION91
4.0163-43.12350.2172610.15913177X-RAY DIFFRACTION95

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