3J07

Model of a 24mer alphaB-crystallin multimer


SOLID-STATE NMR - SOLUTION SCATTERING - ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2KLR 
Solution Scattering Data Acquistion1
Scattering Typex-ray
Radiation/Neutron SourceDESY HAMBURG X33 BEAMLINE
SynchrotronY
Beamline TypeX33
Detector Type2D MAR345
Detector Manufacturer Details
Temperature (K)293
pH7.5
Numer of Time Frames Used1
Protein Concentration Range (mg/mL)0.1-12.6 mg/mL
Sample Bufferphosphate, 100 mM NaCl
Data Reduction SoftwareCBF-PRIMUS
Guiner Mean Radius Of Gyration (nm)5.6
Sigma Mean Radius Of Gyration0.2
R(XS-1) Mean Cross Sectional Radii (nm)
R(XS-1) Sigma Mean Cross Sectional Radii
R(XS-2) Mean Cross Sectional Radii (nm)
R(XS-2) Sigma Mean Cross Sectional Radii
P(R) Protein Length (nm)14.5
Solution Scattering Data Analysis and Model Fitting
MethodSoftwareSoftware AuthorsStarting ModelConformers, Number CalculatedConformers, Number SubmittedConformers, Selection CriteriaBest Representative ConformerOther Details
FITTING OF MODELS WITH SAXS DATA;CHIMERA, PRIMUS, GNOM, XPLOR-NIH, CRYSOL, DISCOVERY STUDIO 1.3;PETOUKHOV, M.V.; SVERGUN, D.I.; SCHWIETERS, C.D. PETTERSON, E.F.; GODDARD, T.D.; ACCELRYS101BEST FIT WITH NMR, SAXS, AND EM DATA1TO DETERMINE HETEROGENEITY, A PYTHON SCRIPT WAS USED TO MODULATE AND FIT THE THEORETICAL SAXS CURVE OF THE MODEL WITH THE EXPERIMENTAL DATA. THE ALGOR ...TO DETERMINE HETEROGENEITY, A PYTHON SCRIPT WAS USED TO MODULATE AND FIT THE THEORETICAL SAXS CURVE OF THE MODEL WITH THE EXPERIMENTAL DATA. THE ALGORITHM THAT WAS APPLIED HAS BEEN PUBLISHED BY MITTELBACH, R. AND GLATTER, O. (1998) IN J. APPL. CRYSTALLOGR. 31:600-608. FOR DETAILS SEE PRIMARY CITATION.
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 13C-13C PDSD18 mg [1,3-13C]-glycerol; U-100% 15N alphaB-crystallin100% H2O7.6270
22D 13C-13C PDSD17 mg [2-13C]-glycerol; U-100% 15N alphaB-crystallin100% H2O7.6270
32D 13C-13C CHHC4 mg [U-100% 13C; U-100% 15N] alphaB-crystallin, 16 mg alphaB-crystallin100% H2O7.6270
42D 13C-13C PDSD4 mg [U-100% 13C; U-100% 15N] alphaB-crystallin, 16 mg alphaB-crystallin100% H2O7.6270
53D 15N-13C-13C NCACX18 mg [1,3-13C]-glycerol; U-100% 15N alphaB-crystallin100% H2O7.6270
63D 15N-13C-13C NCACX17 mg [2-13C]-glycerol; U-100% 15N alphaB-crystallin100% H2O7.6270
73D 15N-13C-13C NCOCX18 mg [1,3-13C]-glycerol; U-100% 15N alphaB-crystallin100% H2O7.6270
83D 15N-13C-13C NCOCX17 mg [2-13C]-glycerol; U-100% 15N alphaB-crystallin100% H2O7.6270
92D 15N-13C TEDOR10 mg [U-100% 15N]; [U-100% 12C] 13C depleted alphaB-crystallin, 10 mg [2-13C]-glycerol; U-100% 15N alphaB-crystallin100% H2O7.6270
102D 15N-13C TEDOR10 mg [U-100% 15N]; [U-100% 12C] 13C depleted alphaB-crystallin, 10 mg [1,3-13C]-glycerol; U-100% 15N alphaB-crystallin100% H2O7.6270
112D 15N-13C NHHC10 mg [U-100% 15N]; [U-100% 12C] 13C depleted alphaB-crystallin, 10 mg [2-13C]-glycerol; U-100% 15N alphaB-crystallin100% H2O7.6270
122D 15N-13C NHHC10 mg [U-100% 15N]; [U-100% 12C] 13C depleted alphaB-crystallin, 10 mg [1,3-13C]-glycerol; U-100% 15N alphaB-crystallin100% H2O7.6270
132D 15N-13C PAIN10 mg [U-100% 15N]; [U-100% 12C] 13C depleted alphaB-crystallin, 10 mg [2-13C]-glycerol; U-100% 15N alphaB-crystallin100% H2O7.6270
142D 1H-13C INEPT4 mg [U-100% 13C; U-100% 15N] alphaB-crystallin, 16 mg alphaB-crystallin100% H2O7.6270
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE400
2BrukerAVANCE600
3BrukerAVANCE700
4BrukerAVANCE900
NMR Refinement
MethodDetailsSoftware
simulated annealing, molecular dynamics, torsion angle dynamicsTHREE DIMERS CONNECTED BY THEIR C-TERMINAL IXI MOTIF WERE FITTED BACK-TO-BACK IN THE EM DENSITY USING CHIMERA. A HEXAMER WAS BUILT FROM MODEL #7 OF PDB ENTRY 2KLR USING NONCRYSTALLOGRAPHIC SYMMETRY RESTRAINTS GIVEN IN THE PDB FILE. DIMERS WERE CONNECTED BY THEIR C-TERMINAL DOMAIN CONTAINING THE IXI-MOTIF, AND THE LINKER (UNP RESIDUES 151-155) WAS ENERGY MINIMIZED USING XPLOR-NIH. THE BETA1/BETA2(FREE) STRUCTURAL SEGMENT WAS PLACED INTO THE EM DENSITY TO FULFILL THE CROSSLINKS FOR A57, S59, AND T63, SIMILAR TO PDB ENTRY 1VLQ. ALPHA2 HELICES OF TWO MONOMERS WERE DOCKED, DEFINING RESIDUES L32, L33, L37, AND F38 AS INTERACTING RESIDUES USING HADDOCK. THE ALPHA2 HELICAL COMPLEX WAS PLACED IN WEAK EM DENSITY AT THE THREE-FOLD AXIS. THE FLEXIBLE C- AND N-TERMINAL RESIDUES, INCLUDING PARTS OF HELIX ALPHA1, WERE PLACED INSIDE THE 24MER TO FIT THE RADIUS OF GYRATION, MEASURED BY SMALL-ANGLE X-RAY SCATTERING IN AN ITERATIVE PROCESS. ALL FRAGMENTS WERE CONNECTED USING DISCOVERY STUDIO 1.6 (ACCELRYS) AND THE LINKERS WERE ENERGY MINIMIZED. BACK PROJECTIONS WERE CALCULATED FOR MODELS OF ALPHAB MULTIMERS CONTAINING 24, 26, AND 28 SUBUNITS USING THE PROGRAM SPIDER. THE CALCULATED PROJECTIONS ARE SIMILAR TO EACH OTHER, TO THE CLASS SUM IMAGES FROM COLLECTED EM DATA, AND TO THOSE CALCULATED FROM THE PUBLISHED EM DENSITY (EMD-1776). DETAILS ARE GIVEN IN THE PRIMARY CITATION.CNS
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number200
Conformers Submitted Total Number1
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionTopSpinBruker Biospin
2processingTopSpinBruker Biospin
3chemical shift assignmentSparkyGoddard
4data analysisSparkyGoddard
5peak pickingSparkyGoddard
6structure solutionX-PLOR NIHSchwieters, Kuszewski, Tjandra and Clore
7dihedral angle determinationTALOSCornilescu, Delaglio and Bax
8structure solutionARIA2.2Rieping W, Habeck M, Bardiaux B, Bernard A, Malliavin TE, Nilges M
9refinementARIA2.2Rieping W, Habeck M, Bardiaux B, Bernard A, Malliavin TE, Nilges M
10structure solutionCNS1.2Brunger, Adams, Clore, Gros, Nilges and Read
11refinementCNS1.2Brunger, Adams, Clore, Gros, Nilges and Read
12structure solutionSOLARIA1(SOLARIA) Fossi M, Castellani F, Nilges M, Oschkinat H, van Rossum BJ
Sample
24mer alphaB-crystallin multimer
Specimen Preparation
Sample Aggregation StatePARTICLE
Staining TypeNEGATIVE
Staining MaterialUranyl Acetate
Staining Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles2565
Reported Resolution (Å)20
Resolution MethodFSC 0.5 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryT
Map-Model Fitting and Refinement
Id1 (2KLR)
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)
Imaging Experiment1
Date of Experiment2008-02-06
Temperature (Kelvin)
Microscope ModelJEOL 100CX
Minimum Defocus (nm)900
Maximum Defocus (nm)1200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification50000
Calibrated Magnification
SourceOTHER
Acceleration Voltage (kV)100
Imaging Details