40S-eIF1-eIF1A-eIF3-eIF3j translation initiation complex from Lachancea kluyveri

Structure of a Yeast 40S-Eif1-Eif1A-Eif3-Eif3J Initiation Complex

THIS DEPOSITION DETAILS AN S. CEREVISIAE MODEL FOR THE CLOSELY RELATED L. KLUYVERI STRUCTURE. INITIAL PLACEMENT OF FOLDED DOMAINS WAS ACCORDING TO THE MASS-SPECTROMETRY MODEL IN DOMAINS WERE FITTED INTO CRYOEM DENSITY LOW-PASS FILTERED AT MEAN LOCAL RESOLUTION AS RIGID BODIES USING CALCULATED DENSITIES GENERATED AT THE SAME RESOLUTION. CORRELATION COEFFICIENT WAS USED AS THE TARGET FUNCTION IN CHIMERA. THE RRM DOMAIN OF EIF3B IS DEPOSITED AS CA TRACE ONLY TO INDICATE THAT ITS POSITION HAS LOWER ANGULAR CONFIDENCE BECAUSE THE DOMAIN IS EXTREMELY SMALL AND GENERATED NO DIRECT CROSS-LINKS TO THE 40S TO AID PLACEMENT. EIF3B HAS BEEN NUMBERED ACCORDING TO THE SECOND START CODON AS THIS IS THOUGHT TO BE THE PREDOMINANT FORM OF THE PROTEIN IN VIVO. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2845.
MAXIMUM A POSTERIORI PROJECTION MATCHING

25 MM K-HEPES, 10 MM MGCL2, 75 MM KCL, 0.5 MM TCEP

LACHANCEA KLUYVERI 40S- EIF1- EIF1A-EIF3-EIF3J INITIATION COMPLEX

VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 75, TEMPERATURE- 120, INSTRUMENT- HOMEMADE PLUNGER, METHOD- 5 SECONDS BLOTTING BEFORE PLUNGING., DETAILS- CARBON FLOATED ON THE SAMPLE PRIOR TO RECOVERY ONTO THE GRID AND FLASH -FREEZING.

SHEET
DETERMINATION METHOD: DSSP
THE SHEETS PRESENTED AS "0A" IN EACH CHAIN ON SHEET RECORDS
BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY
A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS
ARE IDENTICAL.

THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS
BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY
A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS
ARE IDENTICAL.

THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS
BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY
A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS
ARE IDENTICAL.

THE 40S SUBUNIT IS TAKEN FROM PDBS 3U5B,3U5G AND RECHAINED
TO MATCH 2XZM
THE UNIPROT SC EIF3B SEQUENCE USES AN UPSTREAM START CODON
THOUGHT TO BE DISFAVOURED. WE HAVE USED THE NUMBERING
CORRESPONDING TO THE LATER START CODON.