STRUCTURE DETERMINATION OF FELINE PANLEUKOPENIA VIRUS EMPTY PARTICLES

Determination and Refinement of the Canine Parvovirus Empty Capsid Structure

The Canine Parvovirus Empty Capsid Structure

Structure Determination of Monoclinic Canine Parvovirus

Mapping Specific Functions in the Capsid Structure of Canine Parvovirus and Feline Panleukopenia Virus Using Infectious Plasmid Clones

The Three-Dimensional Structure of Canine Parvovirus and its Functional Implications

Preliminary X-Ray Crystallographic Analysis of Canine Parvovirus Crystals

FELINE PANLEUKOPENIA VIRUS (STRAIN B) VIRAL PROTEIN 2

MSDGAVQPDGGQPAVRNERATGSGNGSGGGGGGGSGGVGISTGTFNNQTEFKFLENGWVEITANSSRLVHLNMPESENYK
RVVVNNMDKTAVKGNMALDDIHVEIVTPWSLVDANAWGVWFNPGDWQLIVNTMSELHLVSFEQEIFNVVLKTVSESATQP
PTKVYNNDLTASLMVALDSNNTMPFTPAAMRSETLGFYPWKPTIPTPWRYYFQWDRTLIPSHTGTSGTPTNVYHGTDPDD
VQFYTIENSVPVHLLRTGDEFATGTFFFDCKPCRLTHTWQTNRALGLPPFLNSLPQSEGATNFGDIGVQQDKRRGVTQMG
NTDYITEATIMRPAEVGYSAPYYSFEASTQGPFKTPIAAGRGGAQTDENQAADGDPRYAFGRQHGQKTTTTGETPERFTY
IAHQDTGRYPEGDWIQNINFNLPVTNDNVLLPTDPIGGKTGINYTNIFNTYGPLTALNNVPPVYPNGQIWDKEFDTDLKP
RLHINAPFVCQNNCPGQLFVKVAPNLTNQYDPDASANMSRIVTYSDFWWKGKLVFKAKLRASHTWNPIQQMSINVDNQFN
YVPNNIGAMKIVYEKSQLAPRKLY

Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame

SHEET
THE STRUCTURE OF FELINE PANLEUKOPENIA VIRUS FOLLOWS THE
CANONICAL PICORNAVIRUS "JELLY ROLL" BARREL. THE SHEET
IDENTIFIED AS "BDG" IS THAT REFERRED TO AS "BIDG" IN THE
LITERATURE WITH STRANDS 1 TO 5 CORRESPONDING TO STRANDS
A, B, I, D, AND G. THE SHEET IDENTIFIED AS "CHF" IS THE
SO-CALLED CHEF SHEET WITH STRANDS 1 TO 4 CORRESPONDING TO
STRANDS C, H, E, AND F. THESE TWO SHEETS ARE LOOSELY
CONNECTED TOGETHER BY HYDROGEN BONDS BETWEEN STRAND 4 OF
"CHF" AND RESIDUE 45 IMMEDIATELY PRECEDING STRAND 1 OF
"BDG" OF A FIVE-FOLD RELATED PROTOMER THAT IS NOT
EXPLICITLY PRESENTED ON THE ATOM RECORDS, BUT WHICH CAN BE
GENERATED USING THE SYMMETRY OPERATORS LISTED BELOW. FPV
CONTAINS SEVERAL LONG LOOPS BETWEEN STRANDS OF "BDG" AND
"CHF" WITH LITTLE ORGANIZED SECONDARY STRUCTURE. THERE ARE
STRANDS WITHIN THE LOOPS THAT ARE LOOSELY HYDROGEN-BONDED
TOGETHER. WITH FEWER HYDROGEN BONDS AND LESS REGULAR
SECONDARY STRUCTURE THEY MUST BE REGARDED MORE TENTATIVELY
UNTIL THE STRUCTURE IS REFINED. THIS IS WHY THE SHEET
"LP2" HAS BEEN IDENTIFIED SEPARATELY, ALTHOUGH IT COULD BE
CONSIDERED TO BE AN EXTENSION OF SHEET "CHF", EXTENDING
FROM STRAND 1. STRAND 1 OF "LP2" HAS A BULGE AND A CHANGE
OF DIRECTION AT RESIDUE 107, AFTER WHICH IT BECOMES STRAND
1 OF "CHF". THE MIDDLE STRAND OF "LP2" CONTAINS TWO
SEGMENTS THAT RUN IN THE SAME GENERAL DIRECTION, BUT ARE
SEPARATED BY NON-BETA STRUCTURE. THE FIRST SEGMENT (206
TO 211) HYDROGEN BONDS ON ONE SIDE ONLY, TO RESIDUES 103 TO
111, AND THE SECOND SEGMENT (215 TO 218) HYDROGEN BONDS ON
THE OPPOSITE SIDE TO RESIDUES 230 TO 235.
IN ORDER TO REPRESENT THE BIFURCATED SHEET STRUCTURE IN THE
*SHEET* RECORDS BELOW, TWO SHEETS, *BDG* AND *CDG* ARE
DEFINED. STRANDS 1 - 4 OF THESE SHEETS ARE IDENTICAL.

INTERPRETABLE ELECTRON DENSITY BEGINS AT THE 37TH RESIDUE OF VP2. THERE IS DIFFUSE DENSITY, SUGGESTING THAT ONE IN FIVE OF THE N-TERMINI IS ON THE OUTSIDE OF THE CAPSID, AND THAT THE POLYPEPTIDE RUNS DOWN THE FIVE-FOLD AXIS TO JOIN RESIDUE 37 ON THE INSIDE SURFACE.

icosahedral asymmetric unit, std point frame

PANLEUKEMIA VIRUS COAT PROTEIN, Icosahedral virus, Virus

MAPPAKRARRGLVPPGYKYLGPGNSLDQGEPTNPSDAAAKEHDEAYAAYLRSGKNPYLYFSPADQRFIDQTKDAKDWGGK
IGHYFFRAKKAIAPVLTDTPDHPSTSRPTKPTKRSKPPPHIFINLAKKKKAGAGQVKRDNLAPMSDGAVQPDGGQPAVRN
ERATGSGNGSGGGGGGGSGGVGISTGTFNNQTEFKFLENGWVEITANSSRLVHLNMPESENYKRVVVNNMDKTAVKGNMA
LDDIHVQIVTPWSLVDANAWGVWFNPGDWQLIVNTMSELHLVSFEQEIFNVVLKTVSESATQPPTKVYNNDLTASLMVAL
DSNNTMPFTPAAMRSETLGFYPWKPTIPTPWRYYFQWDRTLIPSHTGTSGTPTNVYHGTDPDDVQFYTIENSVPVHLLRT
GDEFATGTFFFDCKPCRLTHTWQTNRALGLPPFLNSLPQSEGATNFGDIGVQQDKRRGVTQMGNTDYITEATIMRPAEVG
YSAPYYSFEASTQGPFKTPIAAGRGGAQTDENQAADGDPRYAFGRQHGQKTTTTGETPERFTYIAHQDTGRYPEGDWIQN
INFNLPVTNDNVLLPTDPIGGKTGINYTNIFNTYGPLTALNNVPPVYPNGQIWDKEFDTDLKPRLHVNAPFVCQNNCPGQ
LFVKVAPNLTNEYDPDASANMSRIVTYSDFWWKGKLVFKAKLRASHTWNPIQQMSINVDNQFNYVPNNIGAMKIVYEKSQ
LAPRKLY