HEADER TRANSPORT PROTEIN 23-JUL-25 9S35 TITLE CRYO-EM STRUCTURE OF CANDIDA ALBICANS VRG4 BOUND TO AN INHIBITORY TITLE 2 NANOBODY. COMPND MOL_ID: 1; COMPND 2 MOLECULE: LLAMA NANOBODY; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: GDP-MANNOSE TRANSPORTER; COMPND 7 CHAIN: A; COMPND 8 SYNONYM: GMT; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_TAXID: 9844; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: CANDIDA ALBICANS; SOURCE 8 ORGANISM_TAXID: 5476; SOURCE 9 GENE: VRG4, CAALFM_C107700CA, CAO19.1232, CAO19.8817; SOURCE 10 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BJ5460 KEYWDS GDP-MANNOSE TRANSPORTER; MEMBRANE PROTEIN; NUCLEOTIDE SUGAR KEYWDS 2 TRANSPORTER, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.C.DEME,J.L.PARKER,S.M.LEA,S.NEWSTEAD REVDAT 1 03-SEP-25 9S35 0 JRNL AUTH S.NEWSTEAD,J.PARKER,J.DEME,B.FEDDERSEN,S.LEA JRNL TITL STRUCTURAL BASIS FOR TRANSPORT AND INHIBITION OF NUCLEOTIDE JRNL TITL 2 SUGAR TRANSPORT IN PATHOGENIC FUNGI. JRNL REF RES SQ 2025 JRNL REFN ESSN 2693-5015 JRNL PMID 40799752 JRNL DOI 10.21203/RS.3.RS-7213965/V1 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SIMPLE, PHENIX, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.000 REMARK 3 NUMBER OF PARTICLES : 348612 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9S35 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1292149663. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : NANOBODY BOUND TO C.ALBICANS REMARK 245 VRG4 TRANSPORTER REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : TFS FALCON 4I (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A 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 122 REMARK 465 MET A 34 REMARK 465 ASP A 35 REMARK 465 SER A 36 REMARK 465 LYS A 37 REMARK 465 HIS A 38 REMARK 465 SER A 39 REMARK 465 THR A 40 REMARK 465 SER A 41 REMARK 465 SER A 42 REMARK 465 SER A 43 REMARK 465 SER A 44 REMARK 465 SER A 45 REMARK 465 GLY A 46 REMARK 465 SER A 47 REMARK 465 ASP A 194 REMARK 465 ASN A 195 REMARK 465 ALA A 196 REMARK 465 ALA A 197 REMARK 465 VAL A 198 REMARK 465 LYS A 199 REMARK 465 SER A 200 REMARK 465 HIS A 201 REMARK 465 ASP A 202 REMARK 465 GLN A 363 REMARK 465 SER A 364 REMARK 465 GLN A 365 REMARK 465 GLN A 366 REMARK 465 LEU A 367 REMARK 465 PRO A 368 REMARK 465 THR A 369 REMARK 465 THR A 370 REMARK 465 LYS A 371 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 ALA B 90 -179.13 -172.38 REMARK 500 ASN A 54 35.35 -97.52 REMARK 500 THR A 306 -70.13 -93.34 REMARK 500 SER A 307 165.01 178.28 REMARK 500 ILE A 328 -50.40 -120.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-54523 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF CANDIDA ALBICANS VRG4 BOUND TO AN INHIBITORY REMARK 900 NANOBODY. DBREF 9S35 B 0 122 PDB 9S35 9S35 0 122 DBREF 9S35 A 34 371 UNP Q5A477 GMT_CANAL 34 371 SEQRES 1 B 123 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 123 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 123 SER ILE SER GLU ILE ASN VAL MET GLY TRP TYR ARG GLN SEQRES 4 B 123 ALA PRO GLY LYS GLN ARG GLU LEU VAL ALA ARG ILE THR SEQRES 5 B 123 THR GLY GLY SER THR ASN TYR ALA ASP SER VAL LYS GLY SEQRES 6 B 123 ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR VAL SEQRES 7 B 123 TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 B 123 VAL TYR MET CYS ASN ALA HIS ARG ARG VAL VAL MET GLU SEQRES 9 B 123 TRP GLY PRO LEU GLY TYR ASP TYR TRP GLY GLN GLY THR SEQRES 10 B 123 GLN VAL THR VAL SER SER SEQRES 1 A 338 MET ASP SER LYS HIS SER THR SER SER SER SER SER GLY SEQRES 2 A 338 SER LEU ALA THR ARG ILE SER ASN SER GLY PRO ILE SER SEQRES 3 A 338 ILE ALA ALA TYR CYS LEU SER SER ILE LEU MET THR VAL SEQRES 4 A 338 THR ASN LYS TYR VAL LEU SER GLY PHE SER PHE ASN LEU SEQRES 5 A 338 ASN PHE PHE LEU LEU ALA VAL GLN SER ILE VAL CYS ILE SEQRES 6 A 338 VAL THR ILE GLY SER LEU LYS SER LEU ASN ILE ILE THR SEQRES 7 A 338 TYR ARG GLN PHE ASN LYS ASP GLU ALA LYS LYS TRP SER SEQRES 8 A 338 PRO ILE ALA PHE LEU LEU VAL ALA MET ILE TYR THR SER SEQRES 9 A 338 SER LYS ALA LEU GLN TYR LEU SER ILE PRO VAL TYR THR SEQRES 10 A 338 ILE PHE LYS ASN LEU THR ILE ILE LEU ILE ALA TYR GLY SEQRES 11 A 338 GLU VAL ILE TRP PHE GLY GLY LYS VAL THR THR MET ALA SEQRES 12 A 338 LEU SER SER PHE LEU LEU MET VAL LEU SER SER VAL ILE SEQRES 13 A 338 ALA TYR TYR GLY ASP ASN ALA ALA VAL LYS SER HIS ASP SEQRES 14 A 338 ASP ALA PHE ALA LEU TYR LEU GLY TYR PHE TRP MET LEU SEQRES 15 A 338 THR ASN CYS PHE ALA SER ALA ALA PHE VAL LEU ILE MET SEQRES 16 A 338 ARG LYS ARG ILE LYS LEU THR ASN PHE LYS ASP PHE ASP SEQRES 17 A 338 THR MET TYR TYR ASN ASN LEU LEU SER ILE PRO ILE LEU SEQRES 18 A 338 LEU ILE CYS SER PHE ILE PHE GLU ASP TRP SER SER ALA SEQRES 19 A 338 ASN VAL SER LEU ASN PHE PRO ALA ASP ASN ARG VAL THR SEQRES 20 A 338 THR ILE THR ALA MET ILE LEU SER GLY ALA SER SER VAL SEQRES 21 A 338 GLY ILE SER TYR CYS SER ALA TRP CYS VAL ARG VAL THR SEQRES 22 A 338 SER SER THR THR TYR SER MET VAL GLY ALA LEU ASN LYS SEQRES 23 A 338 LEU PRO ILE ALA LEU SER GLY LEU ILE PHE PHE GLU ALA SEQRES 24 A 338 ALA VAL ASN PHE TRP SER VAL SER SER ILE PHE VAL GLY SEQRES 25 A 338 PHE GLY ALA GLY LEU VAL TYR ALA VAL ALA LYS GLN LYS SEQRES 26 A 338 GLN GLN LYS GLU GLN SER GLN GLN LEU PRO THR THR LYS FORMUL 3 HOH *7(H2 O) HELIX 1 AA1 ASP B 60 LYS B 63 5 4 HELIX 2 AA2 LYS B 85 THR B 89 5 5 HELIX 3 AA3 SER A 55 TYR A 76 1 22 HELIX 4 AA4 LEU A 85 LEU A 107 1 23 HELIX 5 AA5 ASN A 116 LEU A 141 1 26 HELIX 6 AA6 SER A 145 ASN A 154 1 10 HELIX 7 AA7 THR A 156 GLY A 169 1 14 HELIX 8 AA8 THR A 173 TYR A 192 1 20 HELIX 9 AA9 ALA A 204 ILE A 232 1 29 HELIX 10 AB1 LYS A 238 LEU A 249 1 12 HELIX 11 AB2 LEU A 249 GLU A 262 1 14 HELIX 12 AB3 SER A 265 PHE A 273 1 9 HELIX 13 AB4 ARG A 278 SER A 291 1 14 HELIX 14 AB5 SER A 292 THR A 306 1 15 HELIX 15 AB6 SER A 307 ASN A 318 1 12 HELIX 16 AB7 LYS A 319 PHE A 330 1 12 HELIX 17 AB8 ASN A 335 LYS A 361 1 27 SHEET 1 AA1 4 VAL B 1 SER B 6 0 SHEET 2 AA1 4 GLY B 15 GLY B 25 -1 O ALA B 22 N VAL B 4 SHEET 3 AA1 4 THR B 76 LEU B 84 -1 O MET B 81 N LEU B 17 SHEET 4 AA1 4 PHE B 66 ASP B 71 -1 N THR B 67 O GLN B 80 SHEET 1 AA2 6 LEU B 10 VAL B 11 0 SHEET 2 AA2 6 THR B 116 VAL B 120 1 O THR B 119 N VAL B 11 SHEET 3 AA2 6 ALA B 90 MET B 102 -1 N ALA B 90 O VAL B 118 SHEET 4 AA2 6 ILE B 30 GLN B 38 -1 N VAL B 32 O HIS B 97 SHEET 5 AA2 6 ARG B 44 THR B 51 -1 O ILE B 50 N MET B 33 SHEET 6 AA2 6 ASN B 57 TYR B 58 -1 O ASN B 57 N ARG B 49 SHEET 1 AA3 4 LEU B 10 VAL B 11 0 SHEET 2 AA3 4 THR B 116 VAL B 120 1 O THR B 119 N VAL B 11 SHEET 3 AA3 4 ALA B 90 MET B 102 -1 N ALA B 90 O VAL B 118 SHEET 4 AA3 4 GLY B 105 TRP B 112 -1 O TYR B 109 N ARG B 98 SSBOND 1 CYS B 21 CYS B 94 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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 TER 953 SER B 121 TER 3356 GLU A 362 HETATM 3357 O HOH B 201 129.869 143.478 144.770 1.00 0.00 O HETATM 3358 O HOH B 202 143.015 143.356 146.110 1.00 26.10 O HETATM 3359 O HOH B 203 129.564 137.809 133.634 1.00 3.02 O HETATM 3360 O HOH A 401 146.751 139.354 151.474 1.00 14.46 O HETATM 3361 O HOH A 402 137.888 151.508 134.483 1.00 21.65 O HETATM 3362 O HOH A 403 144.804 138.502 143.687 1.00 5.27 O HETATM 3363 O HOH A 404 134.687 152.256 137.615 1.00 26.05 O CONECT 151 719 CONECT 719 151 MASTER 163 0 0 17 14 0 0 6 3322 2 2 36 END