[English] 日本語
Yorodumi
- PDB-2y22: Human AlphaB-crystallin Domain (residues 67-157) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y22
TitleHuman AlphaB-crystallin Domain (residues 67-157)
ComponentsALPHA-CRYSTALLIN B
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: 3.7 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 13, 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 / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALPHA-CRYSTALLIN B
B: ALPHA-CRYSTALLIN B
C: ALPHA-CRYSTALLIN B
D: ALPHA-CRYSTALLIN B
E: ALPHA-CRYSTALLIN B
F: ALPHA-CRYSTALLIN B


Theoretical massNumber of molelcules
Total (without water)65,3276
Polymers65,3276
Non-polymers00
Water0
1
A: ALPHA-CRYSTALLIN B


Theoretical massNumber of molelcules
Total (without water)10,8881
Polymers10,8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-CRYSTALLIN B


Theoretical massNumber of molelcules
Total (without water)10,8881
Polymers10,8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ALPHA-CRYSTALLIN B


Theoretical massNumber of molelcules
Total (without water)10,8881
Polymers10,8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ALPHA-CRYSTALLIN B


Theoretical massNumber of molelcules
Total (without water)10,8881
Polymers10,8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: ALPHA-CRYSTALLIN B


Theoretical massNumber of molelcules
Total (without water)10,8881
Polymers10,8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: ALPHA-CRYSTALLIN B


Theoretical massNumber of molelcules
Total (without water)10,8881
Polymers10,8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.280, 78.340, 131.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.44014, -0.52059, 0.73161), (-0.4797, -0.55243, -0.68169), (0.75905, -0.651, -0.00658)-40.65305, -13.10399, 21.90426
2given(-0.64705, -0.69662, -0.30991), (-0.16675, -0.26733, 0.94907), (-0.74399, 0.66577, 0.05681)-30.51887, -68.17198, 21.05918
3given(0.48923, 0.87213, -0.0061), (0.87196, -0.48896, 0.02469), (0.01855, -0.0174, -0.99968)0.09719, -39.3685, 43.45347
4given(-0.56098, 0.82569, -0.05953), (-0.82762, -0.56101, 0.01782), (-0.01868, 0.05927, 0.99807)-18.37072, -28.72197, 44.49226
5given(-0.06013, 0.01077, -0.99813), (0.6723, 0.73957, -0.03252), (0.73784, -0.673, -0.05171)-5.8462, 10.07737, 66.42694

-
Components

#1: Protein
ALPHA-CRYSTALLIN B / 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: 10887.827 Da / Num. of mol.: 6 / Fragment: ALPHA-CRYSTALLIN DOMAIN (ACD), RESIDUES 67-157 / 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
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 137 TO MET ENGINEERED RESIDUE IN CHAIN B, LEU 137 TO MET ...ENGINEERED RESIDUE IN CHAIN A, LEU 137 TO MET ENGINEERED RESIDUE IN CHAIN B, LEU 137 TO MET ENGINEERED RESIDUE IN CHAIN C, LEU 137 TO MET ENGINEERED RESIDUE IN CHAIN D, LEU 137 TO MET ENGINEERED RESIDUE IN CHAIN E, LEU 137 TO MET ENGINEERED RESIDUE IN CHAIN F, LEU 137 TO MET
Sequence detailsL 137 MUTATED TO METHIONINE TO AID IN PHASING ALPHAB CRYSTALLIN DOMAIN RESIDUES 67-157

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 9
Details: SITTING DROPS WITH 20 MG/ML PROTEIN IN 25 MM TRIS, PH 8.5, 200 MM NACL EQUILIBRATED AGAINST 110 MM BICINE, PH 9.0, 55% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 25, 2008 / Details: MIRRORS
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.7→67.4 Å / Num. obs: 7861 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 56.13 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 8.7
Reflection shellResolution: 3.7→3.9 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 4 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y1Y

2y1y


Resolution: 3.7→59.89 Å / Cor.coef. Fo:Fc: 0.8542 / Cor.coef. Fo:Fc free: 0.7946 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.277 361 4.6 %RANDOM
Rwork0.2132 ---
obs0.2162 7846 --
Displacement parametersBiso mean: 88.84 Å2
Baniso -1Baniso -2Baniso -3
1-15.5234 Å20 Å20 Å2
2---23.0258 Å20 Å2
3---7.5023 Å2
Refine analyzeLuzzati coordinate error obs: 0.739 Å
Refinement stepCycle: LAST / Resolution: 3.7→59.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 0 0 3342
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083413HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.074658HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1067SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes533HARMONIC5
X-RAY DIFFRACTIONt_it3413HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion16.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion477SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3437SEMIHARMONIC4
LS refinement shellResolution: 3.7→4.14 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2799 95 4.37 %
Rwork0.2138 2079 -
all0.2167 2174 -

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more