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- PDB-2y1y: Human alphaB crystallin ACD(residues 71-157) -

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Basic information

Entry
Database: PDB / ID: 2y1y
TitleHuman alphaB crystallin ACD(residues 71-157)
ComponentsALPHA-CRYSTALLIN B CHAIN,CRYAB
KeywordsCHAPERONE / SMALL HEAT SHOCK PROTEIN / STRESS PROTEIN / EYE LENS PROTEIN / CATARACT
Function / homology
Function and homology information


microtubule polymerization or depolymerization / negative regulation of intracellular transport / apoptotic process involved in morphogenesis / cardiac myofibril / regulation of programmed cell death / tubulin complex assembly / structural constituent of eye lens / negative regulation of amyloid fibril formation / M band / lens development in camera-type eye ...microtubule polymerization or depolymerization / negative regulation of intracellular transport / apoptotic process involved in morphogenesis / cardiac myofibril / regulation of programmed cell death / tubulin complex assembly / structural constituent of eye lens / negative regulation of amyloid fibril formation / M band / lens development in camera-type eye / muscle organ development / actin filament bundle / HSF1-dependent transactivation / negative regulation of reactive oxygen species metabolic process / negative regulation of protein-containing complex assembly / stress-activated MAPK cascade / muscle contraction / synaptic membrane / response to hydrogen peroxide / cellular response to gamma radiation / negative regulation of cell growth / Z disc / unfolded protein binding / protein folding / response to estradiol / amyloid-beta binding / response to heat / perikaryon / protein refolding / microtubule binding / dendritic spine / lysosome / response to hypoxia / protein stabilization / axon / negative regulation of gene expression / negative regulation of DNA-templated transcription / protein-containing complex binding / negative regulation of apoptotic process / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha-crystallin B chain, ACD domain / Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / Alpha crystallin/Small heat shock protein, animal type / Immunoglobulin-like - #790 / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Immunoglobulin-like ...Alpha-crystallin B chain, ACD domain / Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / Alpha crystallin/Small heat shock protein, animal type / Immunoglobulin-like - #790 / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Alpha-crystallin B chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNaylor, C.E. / Bagneris, C. / Clark, A.R. / Keep, N.H. / Slingsby, C.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: Crystal Structure of R120G Disease Mutant of Human Alphab-Crystallin Domain Dimer Shows Closure of a Groove
Authors: Clark, A.R. / Naylor, C.E. / Bagneris, C. / Keep, N.H. / Slingsby, C.
#1: Journal: J.Mol.Biol. / Year: 2009
Title: Crystal Structures of Alpha-Crystallin Domain Dimers of Alphab-Crystallin and Hsp20.
Authors: Bagneris, C. / Bateman, O.A. / Naylor, C.E. / Cronin, N. / Boelens, W.C. / Keep, N.H. / Slingsby, C.
History
DepositionDec 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 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 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: ALPHA-CRYSTALLIN B CHAIN,
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4282
Polymers10,3101
Non-polymers1181
Water1,13563
1
A: ALPHA-CRYSTALLIN B CHAIN,
hetero molecules

A: ALPHA-CRYSTALLIN B CHAIN,
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8574
Polymers20,6212
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area1490 Å2
ΔGint-33.1 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.030, 36.030, 148.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-2053-

HOH

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Components

#1: Protein ALPHA-CRYSTALLIN B CHAIN, / CRYAB / ALPHAB-CRYSTALLIN / ALPHA(B)-CRYSTALLIN / HEAT SHOCK PROTEIN BETA-5 / HSPB5 / RENAL CARCINOMA ...ALPHAB-CRYSTALLIN / ALPHA(B)-CRYSTALLIN / HEAT SHOCK PROTEIN BETA-5 / HSPB5 / RENAL CARCINOMA ANTIGEN NY-REN-27 / ROSENTHAL FIBER COMPONENT


Mass: 10310.271 Da / Num. of mol.: 1 / Fragment: ALPHA-CRYSTALLIN DOMAIN (ACD), RESIDUES 71-157 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONE CONTAINING PROTEIN / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02511
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 137 TO MSE
Sequence detailsALPHA-CRYSTALLIN DOMAIN ONLY. HUMAN ALPHAB CRYSTALLIN ACD(RESIDUES 71-157). LEUCINE 137 MUTATED TO ...ALPHA-CRYSTALLIN DOMAIN ONLY. HUMAN ALPHAB CRYSTALLIN ACD(RESIDUES 71-157). LEUCINE 137 MUTATED TO METHIONINE FOR PHASING.

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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: 1.99 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 9
Details: SITTING DROPS, 20 MG/ML PROTEIN IN 25 MM TRIS, PH8.5, 200 MM NACL. EQUILIBRATED AGAINST MOTHER LIQUOR OF 110 MM BICINE, PH 9.0, 40% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794
DetectorType: ADSC CCD / Detector: CCD / Date: May 9, 2009 / Details: MIRRORS
RadiationMonochromator: DOUBLE SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→35.01 Å / Num. obs: 7272 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 25.4 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 25.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 26.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 11.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WJ7

2wj7


Resolution: 2→35.012 Å / SU ML: 0.22 / σ(F): 1.37 / Phase error: 18.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2211 588 4.7 %
Rwork0.2044 --
obs0.2051 7272 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.58 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.1894 Å20 Å2-0 Å2
2--3.1894 Å20 Å2
3----6.3788 Å2
Refinement stepCycle: LAST / Resolution: 2→35.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms603 0 8 63 674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003638
X-RAY DIFFRACTIONf_angle_d0.673866
X-RAY DIFFRACTIONf_dihedral_angle_d14.18240
X-RAY DIFFRACTIONf_chiral_restr0.04995
X-RAY DIFFRACTIONf_plane_restr0.003114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.20130.18081580.18482971X-RAY DIFFRACTION100
2.2013-2.51970.24921230.19983034X-RAY DIFFRACTION100
2.5197-3.17430.24841450.20913005X-RAY DIFFRACTION100
3.1743-35.01710.20931620.20552984X-RAY DIFFRACTION100
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)
10.5863-0.0504-0.43710.53870.65332.89650.00520.1148-0.1072-0.2119-0.14050.0473-0.2641-0.0370.14440.15150.1195-0.00050.1684-0.00120.084-16.676514.640811.6912
20.56060.0672-0.55490.66570.09552.8189-0.32770.0825-0.20890.0870.060.03550.82310.4060.15930.26360.16410.02990.25310.01470.1893-10.112.21386.4863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 1:58
2X-RAY DIFFRACTION2CHAIN A AND RESID 59:87

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