HEADER MEMBRANE PROTEIN 14-DEC-21 7QIA TITLE STRUCTURE OF APO-ELENRMT IN COMPLEX WITH TWO NANOBODIES AT 3.5A COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIVALENT METAL CATION TRANSPORTER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NANOBODY 1; COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: NANOBODY 2; COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EGGERTHELLA LENTA; SOURCE 3 ORGANISM_TAXID: 84112; SOURCE 4 GENE: C1853_09580, C1871_08405; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI MC1061; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1211845; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI MC1061; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 1211845; SOURCE 12 MOL_ID: 3; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI MC1061; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 1211845 KEYWDS SLC11, MAGNESIUM, LEUT FOLD, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR K.RAMANADANE,M.S.STRAUB,R.DUTZLER,C.MANATSCHAL REVDAT 2 02-FEB-22 7QIA 1 JRNL REVDAT 1 29-DEC-21 7QIA 0 JRNL AUTH K.RAMANADANE,M.S.STRAUB,R.DUTZLER,C.MANATSCHAL JRNL TITL STRUCTURAL AND FUNCTIONAL PROPERTIES OF A MAGNESIUM JRNL TITL 2 TRANSPORTER OF THE SLC11/NRAMP FAMILY. JRNL REF ELIFE V. 11 2022 JRNL REFN ESSN 2050-084X JRNL PMID 35001872 JRNL DOI 10.7554/ELIFE.74589 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, COOT, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, PHENIX 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 453950 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 7QIA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1292119705. 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 : ELENRMT IN COMPLEX WITH TWO REMARK 245 NANOBODIES; ELENRMT; NANOBODY 1; REMARK 245 NANOBODY 2 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.50 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.00 REMARK 245 SAMPLE DETAILS : THERMOSTABILIZED VERSION REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 22117 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6972.50 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 130000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B 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 MET A 1 REMARK 465 MET A 2 REMARK 465 MET A 3 REMARK 465 LYS A 4 REMARK 465 LYS A 5 REMARK 465 ASN A 6 REMARK 465 GLU A 7 REMARK 465 LYS A 8 REMARK 465 LEU A 9 REMARK 465 GLU A 10 REMARK 465 LEU A 11 REMARK 465 ARG A 12 REMARK 465 ASP A 13 REMARK 465 VAL A 14 REMARK 465 ALA A 15 REMARK 465 VAL A 16 REMARK 465 ASP A 17 REMARK 465 ALA A 18 REMARK 465 ALA A 19 REMARK 465 GLU A 20 REMARK 465 SER A 21 REMARK 465 THR A 22 REMARK 465 GLU A 23 REMARK 465 LEU A 24 REMARK 465 VAL A 25 REMARK 465 GLU A 26 REMARK 465 VAL A 27 REMARK 465 PRO A 28 REMARK 465 GLU A 29 REMARK 465 LYS A 30 REMARK 465 LYS A 31 REMARK 465 GLN A 32 REMARK 465 PRO A 33 REMARK 465 LYS A 34 REMARK 465 LYS A 35 REMARK 465 ILE A 36 REMARK 465 TRP A 37 REMARK 465 SER C 118 REMARK 465 SER C 119 REMARK 465 GLN B 1 REMARK 465 LEU B 2 REMARK 465 SER B 124 REMARK 465 SER B 125 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 A 227 79.40 50.52 REMARK 500 PRO A 228 -12.38 -47.48 REMARK 500 ASP A 247 43.08 -104.75 REMARK 500 TRP A 343 -11.27 73.37 REMARK 500 LYS A 344 18.66 50.18 REMARK 500 ALA A 405 10.23 57.33 REMARK 500 VAL C 48 -56.25 -121.02 REMARK 500 ASN C 83 -163.11 -79.43 REMARK 500 SER C 84 122.25 -39.81 REMARK 500 ARG B 45 146.07 69.83 REMARK 500 VAL B 48 -62.90 -121.57 REMARK 500 ALA B 50 119.31 -160.05 REMARK 500 TRP B 53 -38.14 -131.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-13985 RELATED DB: EMDB REMARK 900 STRUCTURE OF APO-ELENRMT IN COMPLEX WITH TWO NANOBODIES AT 3.5A DBREF1 7QIA A 1 438 UNP A0A369N1S1_EGGLN DBREF2 7QIA A A0A369N1S1 1 438 DBREF 7QIA C 1 119 PDB 7QIA 7QIA 1 119 DBREF 7QIA B 1 125 PDB 7QIA 7QIA 1 125 SEQADV 7QIA GLN A 88 UNP A0A369N1S GLU 88 ENGINEERED MUTATION SEQADV 7QIA SER A 151 UNP A0A369N1S ALA 151 ENGINEERED MUTATION SEQADV 7QIA GLN A 193 UNP A0A369N1S GLU 193 ENGINEERED MUTATION SEQADV 7QIA HIS A 207 UNP A0A369N1S ARG 207 ENGINEERED MUTATION SEQADV 7QIA THR A 244 UNP A0A369N1S SER 244 ENGINEERED MUTATION SEQADV 7QIA VAL A 256 UNP A0A369N1S ILE 256 ENGINEERED MUTATION SEQADV 7QIA ALA A 275 UNP A0A369N1S SER 275 ENGINEERED MUTATION SEQADV 7QIA ILE A 366 UNP A0A369N1S VAL 366 ENGINEERED MUTATION SEQADV 7QIA ILE A 385 UNP A0A369N1S VAL 385 ENGINEERED MUTATION SEQADV 7QIA LEU A 418 UNP A0A369N1S VAL 418 ENGINEERED MUTATION SEQADV 7QIA ALA A 429 UNP A0A369N1S VAL 429 ENGINEERED MUTATION SEQRES 1 A 438 MET MET MET LYS LYS ASN GLU LYS LEU GLU LEU ARG ASP SEQRES 2 A 438 VAL ALA VAL ASP ALA ALA GLU SER THR GLU LEU VAL GLU SEQRES 3 A 438 VAL PRO GLU LYS LYS GLN PRO LYS LYS ILE TRP LEU LEU SEQRES 4 A 438 LEU ALA ALA LEU GLY PRO GLY ILE VAL THR ALA MET ALA SEQRES 5 A 438 GLY ASN ASP ALA GLY GLY ILE SER THR TYR SER THR VAL SEQRES 6 A 438 GLY ALA LYS PHE GLY PHE ALA THR LEU TRP VAL ILE PRO SEQRES 7 A 438 ILE MET CYS VAL LEU LEU ILE VAL VAL GLN MET THR ALA SEQRES 8 A 438 ALA ARG MET GLY ALA VAL THR GLY LYS GLY PHE ALA ALA SEQRES 9 A 438 LEU ILE ARG GLU ARG PHE GLY ILE ARG LEU THR ALA LEU SEQRES 10 A 438 ALA MET LEU ALA LEU LEU ILE GLY ASN VAL ALA THR THR SEQRES 11 A 438 PHE SER GLU PHE ALA GLY ILE ALA SER GLY MET GLU MET SEQRES 12 A 438 PHE GLY VAL SER LYS TYR LEU SER VAL PRO VAL ALA ALA SEQRES 13 A 438 VAL ALA VAL TRP LEU LEU VAL VAL GLY GLY SER TYR LYS SEQRES 14 A 438 ARG VAL GLU LYS VAL PHE LEU ILE LEU SER LEU VAL PHE SEQRES 15 A 438 VAL THR TYR ILE VAL ALA ALA PHE MET ALA GLN PRO ASN SEQRES 16 A 438 TRP GLU GLU ALA LEU THR SER THR VAL VAL PRO HIS ILE SEQRES 17 A 438 VAL ASN ASP GLN SER PHE VAL SER LEU VAL ILE ALA MET SEQRES 18 A 438 ILE GLY THR THR ILE ALA PRO TRP MET MET PHE PHE ASN SEQRES 19 A 438 GLN SER ASN VAL VAL GLU LYS GLY VAL THR VAL LYS ASP SEQRES 20 A 438 LEU PHE SER GLN LYS VAL ASP VAL VAL ALA GLY THR ILE SEQRES 21 A 438 ALA ALA CYS LEU VAL ALA TRP PHE ILE ILE VAL THR THR SEQRES 22 A 438 GLY ALA VAL LEU PHE PRO GLN GLY ILE GLU ILE GLU SER SEQRES 23 A 438 ALA ALA ASP ALA ALA ARG ALA LEU ALA PRO PHE ALA GLY SEQRES 24 A 438 HIS TYR ALA GLU ALA LEU PHE ALA ILE GLY LEU ILE ALA SEQRES 25 A 438 ALA SER PHE LEU ALA ALA CYS VAL LEU PRO LEU THR THR SEQRES 26 A 438 ALA PHE VAL ILE CYS GLU ALA PHE GLY TRP GLU ALA GLY SEQRES 27 A 438 VAL SER PHE LYS TRP LYS GLU ALA PRO LEU PHE LYS SER SEQRES 28 A 438 ILE PHE THR PHE VAL ILE ALA PHE SER ALA VAL VAL VAL SEQRES 29 A 438 LEU ILE PRO ASN ILE ASP LEU MET GLY VAL MET LEU THR SEQRES 30 A 438 ALA GLN PHE VAL ASN GLY LEU ILE LEU PRO VAL LEU LEU SEQRES 31 A 438 VAL PHE MET ALA ILE ILE ALA ALA ASP LYS ARG VAL MET SEQRES 32 A 438 GLY ALA TYR ARG SER ARG ILE VAL SER ARG VAL LEU ILE SEQRES 33 A 438 TRP LEU THR VAL GLY ILE VAL THR VAL LEU THR ALA ALA SEQRES 34 A 438 LEU LEU VAL MET GLN VAL LEU GLY ILE SEQRES 1 C 119 GLN LEU GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 C 119 PRO GLY GLY SER LEU ARG LEU SER CYS GLU ALA SER GLY SEQRES 3 C 119 LYS VAL PHE MET ILE ASN ALA MET GLY TRP TYR ARG GLN SEQRES 4 C 119 ALA PRO GLY LYS GLN ARG GLU LEU VAL ALA PHE ILE SER SEQRES 5 C 119 ARG ARG GLY ASN ILE ASN TYR ALA ASP SER VAL LYS GLY SEQRES 6 C 119 ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR VAL SEQRES 7 C 119 TYR LEU GLN MET ASN SER LEU ARG PRO GLU ASP THR ALA SEQRES 8 C 119 ILE TYR TYR CYS SER ALA ASP PRO ARG SER ASN LEU ASP SEQRES 9 C 119 ASP GLY ARG TYR TRP GLY LYS GLY THR PRO VAL THR VAL SEQRES 10 C 119 SER SER SEQRES 1 B 125 GLN LEU GLN LEU VAL GLU SER GLY GLY GLY LEU VAL LEU SEQRES 2 B 125 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER VAL SEQRES 3 B 125 ARG THR PHE SER HIS TYR ALA LEU GLY TRP PHE ARG GLN SEQRES 4 B 125 ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA ALA ILE ARG SEQRES 5 B 125 TRP THR GLY SER SER ALA ASN TYR ALA ASP SER VAL LYS SEQRES 6 B 125 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 B 125 VAL ASP LEU ARG MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 B 125 ALA VAL TYR TYR CYS ALA ALA ARG THR VAL TYR ARG PRO SEQRES 9 B 125 GLY PHE GLU ASP PRO ASN GLU TYR ALA TYR TRP GLY GLN SEQRES 10 B 125 GLY THR ARG VAL THR VAL SER SER FORMUL 4 HOH *3(H2 O) HELIX 1 AA1 LEU A 38 GLY A 53 1 16 HELIX 2 AA2 ASP A 55 PHE A 69 1 15 HELIX 3 AA3 GLY A 70 LEU A 74 5 5 HELIX 4 AA4 TRP A 75 GLY A 99 1 25 HELIX 5 AA5 GLY A 101 PHE A 110 1 10 HELIX 6 AA6 GLY A 111 MET A 143 1 33 HELIX 7 AA7 SER A 151 GLY A 165 1 15 HELIX 8 AA8 SER A 167 SER A 179 1 13 HELIX 9 AA9 LEU A 180 ALA A 192 1 13 HELIX 10 AB1 ASN A 195 SER A 202 1 8 HELIX 11 AB2 ASP A 211 ILE A 226 1 16 HELIX 12 AB3 ALA A 227 GLY A 242 1 16 HELIX 13 AB4 THR A 244 LYS A 246 5 3 HELIX 14 AB5 ASP A 247 LEU A 277 1 31 HELIX 15 AB6 SER A 286 ARG A 292 1 7 HELIX 16 AB7 LEU A 294 GLY A 299 1 6 HELIX 17 AB8 TYR A 301 PHE A 333 1 33 HELIX 18 AB9 ALA A 346 LEU A 365 1 20 HELIX 19 AC1 ASP A 370 ALA A 398 1 29 HELIX 20 AC2 ARG A 409 GLY A 437 1 29 HELIX 21 AC3 THR B 28 TYR B 32 5 5 HELIX 22 AC4 ASP B 62 LYS B 65 5 4 HELIX 23 AC5 ASP B 108 TYR B 112 5 5 SHEET 1 AA1 4 LEU C 2 GLY C 8 0 SHEET 2 AA1 4 LEU C 18 GLY C 26 -1 O SER C 21 N SER C 7 SHEET 3 AA1 4 THR C 77 MET C 82 -1 O LEU C 80 N LEU C 20 SHEET 4 AA1 4 PHE C 67 ASP C 72 -1 N THR C 68 O GLN C 81 SHEET 1 AA2 2 ALA C 33 MET C 34 0 SHEET 2 AA2 2 ALA C 97 ASP C 98 -1 O ASP C 98 N ALA C 33 SHEET 1 AA3 2 ALA C 91 TYR C 93 0 SHEET 2 AA3 2 THR C 113 VAL C 115 -1 O THR C 113 N TYR C 93 SHEET 1 AA4 2 LEU B 18 LEU B 20 0 SHEET 2 AA4 2 ARG B 82 ASN B 84 -1 O ARG B 82 N LEU B 20 SHEET 1 AA5 5 ALA B 58 TYR B 60 0 SHEET 2 AA5 5 GLU B 46 ILE B 51 -1 N ALA B 50 O ASN B 59 SHEET 3 AA5 5 GLY B 35 ARG B 38 -1 N TRP B 36 O ALA B 49 SHEET 4 AA5 5 ALA B 92 CYS B 96 -1 O TYR B 95 N PHE B 37 SHEET 5 AA5 5 THR B 119 VAL B 121 -1 O VAL B 121 N ALA B 92 SSBOND 1 CYS C 22 CYS C 95 1555 1555 2.03 SSBOND 2 CYS B 22 CYS B 96 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