9GIV | pdb_00009giv

Structure of the human mitochondrial pyruvate carrier inhibited by a UK5099-derivative


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldAF-Q9Y5U8-F1-model_v4_MPC1.pdb 
in silico modelAlphaFoldAF-O95563-F1-model_v4_MPC2.pdb 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg10.701
r_long_range_B_refined5.576
r_long_range_B_other5.576
r_dihedral_angle_1_deg5.066
r_dihedral_angle_2_deg4.865
r_mcangle_it1.817
r_mcangle_other1.816
r_angle_refined_deg1.573
r_scangle_other1.146
r_mcbond_it0.965
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg10.701
r_long_range_B_refined5.576
r_long_range_B_other5.576
r_dihedral_angle_1_deg5.066
r_dihedral_angle_2_deg4.865
r_mcangle_it1.817
r_mcangle_other1.816
r_angle_refined_deg1.573
r_scangle_other1.146
r_mcbond_it0.965
r_mcbond_other0.965
r_angle_other_deg0.551
r_scbond_it0.542
r_scbond_other0.542
r_chiral_restr0.081
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.001
r_bond_other_d
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Sample
Complex of human mitochondrial pyruvate carrier (MPC1L/MPC2) inhibited by a UK5099-derivative with a pro-macrobody
Sample Components
Mitochondrial pyruvate carrier (MPC1L/MPC2)
Pro-macrobody (fusion of a nanobody with Maltose-binding protein)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles136967
Reported Resolution (Å)3.65
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetCross-correlation coefficient
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeTFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)54.68
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)600
Maximum Defocus (nm)1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification165000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONWarp
IMAGE ACQUISITIONEPU
CTF CORRECTIONWarp
MODEL FITTINGCoot0.9.8.92
MODEL FITTINGISOLDE
MODEL FITTINGUCSF ChimeraX1.7.1
INITIAL EULER ASSIGNMENTcryoSPARC3.3.2
FINAL EULER ASSIGNMENTcryoSPARC3.3.2
CLASSIFICATIONcryoSPARC3.3.2
RECONSTRUCTIONcryoSPARC3.3.2
MODEL REFINEMENTREFMAC5.8.0419
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION763859