1QGC | pdb_00001qgc

STRUCTURE OF THE COMPLEX OF A FAB FRAGMENT OF A NEUTRALIZING ANTIBODY WITH FOOT AND MOUTH DISEASE VIRUS

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FMD

Sample
FAB FRAGMENT OF A NEUTRALIZING ANTIBODY WITH FOOT AND MOUTH DISEASE VIRUS

Specimen Preparation
Sample Aggregation State	PARTICLE

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles
Reported Resolution (Å)	30
Resolution Method
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1FMD)
Refinement Space	REAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details	DETAILS--THE ATOMIC MODEL WAS GENERATED USING THE 3D MAP DETERMINED BY CRYO-ELECTRON MICROSCOPY. X-RAY ATOMIC STRUCTURES WERE AVAILABLE FOR THE INTAC ...	DETAILS--THE ATOMIC MODEL WAS GENERATED USING THE 3D MAP DETERMINED BY CRYO-ELECTRON MICROSCOPY. X-RAY ATOMIC STRUCTURES WERE AVAILABLE FOR THE INTACT PARTICLE OF FMDV-C AND THE SD6 FAB CO-CRYSTALLIZED WITH A SYNTHETIC PEPTIDE CORRESPONDING TO THE DOMINANT ANTIGENIC LOOP, THE GH LOOP, FROM THE VIRAL CAPSIDE PROTEIN VP1. THE ATOMIC MODEL WAS OBTAINED BY DOCKING THE TWO CRYSTALLOGRAPHIC STRUCTURES IN THE RECONSTRUCTED EM MAP. FITTING WAS DONE SIMULTANEOUSLY IN REAL AND RECIPROCAL SPACE. IN REAL SPACE THE CALCULATED ELECTRON DENSITY FOR THE STARTING MODELS WERE FITTED INTO THE CRYO-EM DENSITY BY A STEEPEST DESCENT PROCEDURE WHICH OPTIMIZED THE LINEAR CORRELATION COEFFICIENT BETWEEN THE TWO DISTRIBUTION (GAP- J.GRIMES,D.STUART, UNPUBLISHED) FOR THE RECIPROCAL SPACE FITTING THE STRUCTURE FACTORS CORRESPONDING TO THE CRYO-EM DENSITY OF THE COMPLEX WERE CALCULATED BY INVERSE FOURIER TRANSFORMATIONS AND THESE FACTORS AND PHASES WERE USED TO REFINE THE X-RAY STRUCTURES, BY RIGID BODY MINIMIZATION, USING X-PLOR (BRUNGER, ET.AL., 1993, YALE UNIVERSITY)

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	20

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	JEOL 2000EXII
Minimum Defocus (nm)	1800
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	30000
Calibrated Magnification
Source
Acceleration Voltage (kV)	100
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	GAP
MODEL FITTING	X-PLOR
RECONSTRUCTION	MRC

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.