The pseudo-atomic structure of dengue immature virus in complex with Fab fragments of the anti-fusion loop antibody E53

Structural basis for the preferential recognition of immature flaviviruses by a fusion-loop antibody

REFINEMENT PROTOCOL--Rigid Body DETAILS--Each E molecule was divided into two rigid bodies, DI-DIII and DII-pr

( Details about the particle: 400 mesh copper grid )

T1 icosahedron with three E monomers and two Fab per asymmetric unit
Immature Dengue Virus complexed with E53 Fab

A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.

prM, Peptide pr, Small envelope protein M, Matrix protein, Envelope protein E, Non-structural protein 1, NS1

MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTESRCPTQGEP
SLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFRCKKNMEGKVVQPENLEYTVVITPHSGEEHAVGNDTGKHGK
EVKITPQSSITEAELTGYGTVTMECSPRTGLDFNEMVLLQMENKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTF
KNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKVVKEIAETQHGTI
VIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLDWFKKG

FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTITYKCPLLRQNEPEDIDCWCNSTSTWVTYGTC
T

EVKLVESGGGLVLPGGSLRLSCATSGFTFTDYYMTWVRQPPGKALEWLGFIGNKANDYTTEYSASVKGRFTISRDDSQSI
LYLQMSTLRAEDRATYYCATVYGNYPYFDVWGAGTTVAVSSAKTTPPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTL
TWNSGSLSSGVHTFPAVLQSGLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMHWYQQKSGTSPKIWIYESSKLASGVPVRFSGSGSGTSYSLTISSMEAE
DVATYYCQQWSSHPHPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGV
LNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

icosahedral asymmetric unit, std point frame

Dengue Virus, DENV, immature, fusion loop, Fab, E53, ATP-binding, Envelope protein, Helicase, Hydrolase, Membrane, Nucleotide-binding, RNA replication, Transmembrane, Virion, Capsid protein, Cleavage on pair of basic residues, Core protein, Endoplasmic reticulum, Glycoprotein, Secreted, VIRUS

MRCIGMSNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTESRCPTQGEP
SLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFRCKKNMEGKVVQPENLEYTIVITPHSGEEHAVGNDTGKHGK
EIKITPQSSITEAELTGYGTVTMECSPRTGLDFNEMVLLQMENKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTF
KNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKVVKEIAETQHGTI
VIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKG