HEADER CELL ADHESION 09-JAN-16 5FT2 TITLE SUB-TOMOGRAM AVERAGING OF LASSA VIRUS GLYCOPROTEIN SPIKE FROM VIRUS- TITLE 2 LIKE PARTICLES AT PH 5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRE-GLYCOPROTEIN POLYPROTEIN GP COMPLEX; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN, UNP RESIDUES 75-237; COMPND 5 SYNONYM: GP1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LASSA VIRUS; SOURCE 3 ORGANISM_COMMON: LASSA MAMMARENAVIRUS, LASV; SOURCE 4 ORGANISM_TAXID: 11622; SOURCE 5 STRAIN: JOSIAH; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111 KEYWDS CELL ADHESION, MEMBRANE PROTEIN, GLYCOPROTEIN, RECEPTOR BINDING, KEYWDS 2 MEMBRANE FUSION EXPDTA ELECTRON MICROSCOPY AUTHOR S.LI,S.ZHAOYANG,R.PRYCE,M.L.PARSY,S.K.FEHLING,K.SCHLIE,C.A.SIEBERT, AUTHOR 2 W.GARTEN,T.A.BOWDEN,T.STRECKER,J.T.HUISKONEN REVDAT 4 29-JUL-20 5FT2 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 30-AUG-17 5FT2 1 REMARK REVDAT 2 02-AUG-17 5FT2 1 REVDAT 1 02-MAR-16 5FT2 0 JRNL AUTH S.LI,Z.SUN,R.PRYCE,M.PARSY,S.K.FEHLING,K.SCHLIE,C.A.SIEBERT, JRNL AUTH 2 W.GARTEN,T.A.BOWDEN,T.STRECKER,J.T.HUISKONEN JRNL TITL ACIDIC PH-INDUCED CONFORMATIONS AND LAMP1 BINDING OF THE JRNL TITL 2 LASSA VIRUS GLYCOPROTEIN SPIKE. JRNL REF PLOS PATHOG. V. 12 5418 2016 JRNL REFN ISSN 1553-7366 JRNL PMID 26849049 JRNL DOI 10.1371/JOURNAL.PPAT.1005418 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.COHEN-DVASHI,N.COHEN,H.ISRAELI,R.DISKIN REMARK 1 TITL MOLECULAR MECHANISM FOR LAMP1 RECOGNITION BY LASSA VIRUS. REMARK 1 REF J.VIROL. V. 89 7584 2015 REMARK 1 REFN ISSN 0022-538X REMARK 1 PMID 25972533 REMARK 1 DOI 10.1128/JVI.00651-15 REMARK 2 REMARK 2 RESOLUTION. 16.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : UCSF CHIMERA, DYNAMO, IMOD, UCSF REMARK 3 CHIMERA REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 4ZJF REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 2.700 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 16.40 REMARK 3 NUMBER OF PARTICLES : 2578 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: SUB-TOMOGRAM AVERAGING SUBMISSION BASED ON REMARK 3 EXPERIMENTAL DATA FROM EMDB EMD-3292. (DEPOSITION ID: 14158). REMARK 4 REMARK 4 5FT2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE. REMARK 100 THE DEPOSITION ID IS D_1290065998. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : TOMOGRAPHY REMARK 245 SPECIMEN TYPE : CRYO-EM REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : PURIFIED LASSA VIRUS VLPS AT PH REMARK 245 5 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : VITRIFICATION 1 -- CRYOGEN- REMARK 245 ETHANE-PROPANE MIXTURE, REMARK 245 HUMIDITY- 80, TEMPERATURE- 120, REMARK 245 INSTRUMENT- GATAN CRYOPLUNGE 3, REMARK 245 METHOD- BLOT FOR 3 SECONDS REMARK 245 BEFORE PLUNGING., REMARK 245 SAMPLE BUFFER : 50 MM BUFFER OF SUCCINIC ACID, REMARK 245 DIHYDROGEN PHOSPHATE AND REMARK 245 GLYCINE (SPG) REMARK 245 PH : 5.20 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 25-SEP-14 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TECNAI F30 REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 2800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 6700.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : -45.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 45.00 REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 60.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 160000 REMARK 245 CALIBRATED MAGNIFICATION : 37037 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : SUPER-RESOLUTION COUNTING REMARK 245 MODE REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER B 66 REMARK 465 HIS B 67 REMARK 465 HIS B 68 REMARK 465 HIS B 69 REMARK 465 HIS B 70 REMARK 465 HIS B 71 REMARK 465 HIS B 72 REMARK 465 GLY B 73 REMARK 465 GLY B 74 REMARK 465 MET B 75 REMARK 465 GLU B 76 REMARK 465 THR B 77 REMARK 465 LEU B 78 REMARK 465 ASN B 79 REMARK 465 MET B 80 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 420 O HOH B 422 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU B 120 59.63 -90.19 REMARK 500 SER B 169 68.92 -110.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-3292 RELATED DB: EMDB DBREF 5FT2 B 75 237 UNP P08669 GLYC_LASSJ 75 237 SEQADV 5FT2 SER B 66 UNP P08669 EXPRESSION TAG SEQADV 5FT2 HIS B 67 UNP P08669 EXPRESSION TAG SEQADV 5FT2 HIS B 68 UNP P08669 EXPRESSION TAG SEQADV 5FT2 HIS B 69 UNP P08669 EXPRESSION TAG SEQADV 5FT2 HIS B 70 UNP P08669 EXPRESSION TAG SEQADV 5FT2 HIS B 71 UNP P08669 EXPRESSION TAG SEQADV 5FT2 HIS B 72 UNP P08669 EXPRESSION TAG SEQADV 5FT2 GLY B 73 UNP P08669 EXPRESSION TAG SEQADV 5FT2 GLY B 74 UNP P08669 EXPRESSION TAG SEQRES 1 B 172 SER HIS HIS HIS HIS HIS HIS GLY GLY MET GLU THR LEU SEQRES 2 B 172 ASN MET THR MET PRO LEU SER CYS THR LYS ASN ASN SER SEQRES 3 B 172 HIS HIS TYR ILE MET VAL GLY ASN GLU THR GLY LEU GLU SEQRES 4 B 172 LEU THR LEU THR ASN THR SER ILE ILE ASN HIS LYS PHE SEQRES 5 B 172 CYS ASN LEU SER ASP ALA HIS LYS LYS ASN LEU TYR ASP SEQRES 6 B 172 HIS ALA LEU MET SER ILE ILE SER THR PHE HIS LEU SER SEQRES 7 B 172 ILE PRO ASN PHE ASN GLN TYR GLU ALA MET SER CYS ASP SEQRES 8 B 172 PHE ASN GLY GLY LYS ILE SER VAL GLN TYR ASN LEU SER SEQRES 9 B 172 HIS SER TYR ALA GLY ASP ALA ALA ASN HIS CYS GLY THR SEQRES 10 B 172 VAL ALA ASN GLY VAL LEU GLN THR PHE MET ARG MET ALA SEQRES 11 B 172 TRP GLY GLY SER TYR ILE ALA LEU ASP SER GLY ARG GLY SEQRES 12 B 172 ASN TRP ASP CYS ILE MET THR SER TYR GLN TYR LEU ILE SEQRES 13 B 172 ILE GLN ASN THR THR TRP GLU ASP HIS CYS GLN PHE SER SEQRES 14 B 172 ARG PRO SER MODRES 5FT2 ASN B 109 ASN GLYCOSYLATION SITE MODRES 5FT2 ASN B 119 ASN GLYCOSYLATION SITE MODRES 5FT2 ASN B 167 ASN GLYCOSYLATION SITE MODRES 5FT2 ASN B 224 ASN GLYCOSYLATION SITE HET NAG A 1 14 HET NAG A 2 14 HET NAG C 1 14 HET NAG C 2 14 HET NAG B 303 14 HET NAG B 304 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE FORMUL 2 NAG 6(C8 H15 N O6) FORMUL 6 HOH *23(H2 O) HELIX 1 1 ASP B 122 PHE B 140 1 19 HELIX 2 2 TYR B 172 HIS B 179 1 8 HELIX 3 3 THR B 182 ALA B 195 1 14 SHEET 1 BA 5 SER B 91 ILE B 95 0 SHEET 2 BA 5 GLY B 102 THR B 108 -1 O LEU B 103 N ILE B 95 SHEET 3 BA 5 TYR B 219 THR B 225 -1 O TYR B 219 N THR B 108 SHEET 4 BA 5 LYS B 161 ASN B 167 -1 O ILE B 162 N ASN B 224 SHEET 5 BA 5 ALA B 152 ASN B 158 -1 O ALA B 152 N ASN B 167 SHEET 1 BB 2 ILE B 201 ASP B 204 0 SHEET 2 BB 2 ASP B 211 MET B 214 -1 O CYS B 212 N LEU B 203 SSBOND 1 CYS B 86 CYS B 231 1555 1555 2.04 SSBOND 2 CYS B 118 CYS B 155 1555 1555 2.04 SSBOND 3 CYS B 180 CYS B 212 1555 1555 2.04 LINK ND2 ASN B 109 C1 NAG A 1 1555 1555 1.44 LINK ND2 ASN B 119 C1 NAG B 304 1555 1555 1.44 LINK ND2 ASN B 167 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN B 224 C1 NAG B 303 1555 1555 1.43 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.43 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000