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- PDB-2y1z: Human alphaB Crystallin ACD R120G -

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Basic information

Entry
Database: PDB / ID: 2y1z
TitleHuman alphaB Crystallin ACD R120G
ComponentsALPHA-CRYSTALLIN B CHAIN
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 / regulation of programmed cell death / cardiac myofibril / structural constituent of eye lens / tubulin complex assembly / negative regulation of amyloid fibril formation / lens development in camera-type eye / M band ...microtubule polymerization or depolymerization / negative regulation of intracellular transport / apoptotic process involved in morphogenesis / regulation of programmed cell death / cardiac myofibril / structural constituent of eye lens / tubulin complex assembly / negative regulation of amyloid fibril formation / lens development in camera-type eye / M band / muscle organ development / actin filament bundle / negative regulation of reactive oxygen species metabolic process / HSF1-dependent transactivation / stress-activated MAPK cascade / negative regulation of protein-containing complex assembly / muscle contraction / synaptic membrane / glutathione metabolic process / response to hydrogen peroxide / cellular response to gamma radiation / negative regulation of cell growth / Z disc / : / response to estradiol / amyloid-beta binding / response to heat / protein refolding / protein folding / microtubule binding / dendritic spine / perikaryon / response to hypoxia / lysosome / protein stabilization / negative regulation of gene expression / axon / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / protein-containing complex binding / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
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 ...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: 2.5 Å
AuthorsClark, A.R. / Bagneris, C. / Naylor, C.E. / 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 1, 2024Group: 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
B: ALPHA-CRYSTALLIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7676
Polymers21,2942
Non-polymers4734
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-45.9 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.730, 60.730, 100.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUGLUGLUAA70 - 1057 - 42
21LEULEUGLUGLUBB70 - 1057 - 42
12ARGARGVALVALAA116 - 14553 - 82
22ARGARGVALVALBB116 - 14553 - 82

NCS oper: (Code: given
Matrix: (-0.996, -0.088, 0.032), (-0.086, 0.994, 0.062), (-0.037, 0.059, -0.998)
Vector: 60.047, 1.95, 15.329)

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Components

#1: Protein ALPHA-CRYSTALLIN B CHAIN / 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: 10646.999 Da / Num. of mol.: 2 / Fragment: ALPHA-CRYSTALLIN DOMAIN (ACD), RESIDUES 67-157 / Mutation: YES
Source method: isolated from a genetically manipulated source
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


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


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


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 120 TO HIS ENGINEERED RESIDUE IN CHAIN A, LEU 137 TO SER ...ENGINEERED RESIDUE IN CHAIN A, ARG 120 TO HIS ENGINEERED RESIDUE IN CHAIN A, LEU 137 TO SER ENGINEERED RESIDUE IN CHAIN B, ARG 120 TO HIS ENGINEERED RESIDUE IN CHAIN B, LEU 137 TO SER
Sequence detailsR120G IS A DISEASE ASSOCIATED MUTATION L137M TO ALLOW CRYSTALISATION. ALPHA-CRYSTALLIN DOMAIN ONLY. ...R120G IS A DISEASE ASSOCIATED MUTATION L137M TO ALLOW CRYSTALISATION. ALPHA-CRYSTALLIN DOMAIN ONLY. HUMAN ALPHAB CRYSTALLIN ACD(RESIDUES 67-157)

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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: 2.49 Å3/Da / Density % sol: 50.6 % / Description: NONE
Crystal growpH: 7.4
Details: PROTEIN AT 16.5 MG/ML IN BUFFER (25 MM TRISHCL, PH 7.5, 25 MM NACL) WAS MIXED 1:1 WITH MOTHER LIQUOR (36% MPD, 0.18M POTASSIUM CHLORIDE)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 24, 2010 / Details: MIRRORS
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
111.000H, 1.000K, L10.53
11-1.000H, -1.000K, L20.47
ReflectionResolution: 2.5→46.6 Å / Num. obs: 7582 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 43.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.3 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN ALPHA-CRYSTALLIN DOMAIN RESIDUES 71- 157

Resolution: 2.5→36.27 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.892 / SU B: 18.426 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24052 788 10.4 %RANDOM
Rwork0.17335 ---
obs0.18047 6777 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.194 Å2
Baniso -1Baniso -2Baniso -3
1-6.51 Å20 Å20 Å2
2--6.51 Å20 Å2
3----13.02 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1340 0 32 14 1386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0211416
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9641.9781915
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3385176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64223.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40515243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0551512
X-RAY DIFFRACTIONr_chiral_restr0.0640.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211068
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2131.5862
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.4121395
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.6623554
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1284.5517
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 495 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.415
2Bloose positional0.415
1Aloose thermal2.4950
2Bloose thermal2.4950
LS refinement shellResolution: 2.499→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 58 -
Rwork0.219 469 -
obs--93.77 %
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)
15.5770.3762-1.85952.2609-0.63512.5683-0.02030.041-0.04420.0177-0.05370.01670.09870.01690.0740.0695-0.0067-0.01920.0601-0.03520.035323.8861-12.264916.8092
22.0483-0.7175-1.13111.42920.80621.6936-0.01350.0401-0.08670.0423-0.0278-0.0799-0.0595-0.16540.04130.07620.0213-0.0330.08710.03390.069636.8936-10.6911-3.1666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A67 - 151
2X-RAY DIFFRACTION2B65 - 150

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