HEADER PROTEIN FIBRIL 18-AUG-21 7RVI TITLE SEGMENT FROM NAKED MOLE RAT (ELK T174S) PRION PROTEIN 168-176 TITLE 2 QYNNQNSFV COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR PRION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 158-166; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HETEROCEPHALUS GLABER; SOURCE 4 ORGANISM_COMMON: NAKED MOLE RAT; SOURCE 5 ORGANISM_TAXID: 10181 KEYWDS AMYLOID, PRION, FIBRIL, NAKED MOLE RAT, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR C.GLYNN,J.A.RODRIGUEZ,E.HERNANDEZ REVDAT 2 22-MAY-24 7RVI 1 REMARK REVDAT 1 24-AUG-22 7RVI 0 JRNL AUTH C.GLYNN,E.HERNANDEZ,M.GALLAGHER-JONES,J.MIAO,J.A.RODRIGUEZ JRNL TITL STRUCTURAL AND BIOPHYSICAL CONSEQUENCES OF SEQUENCE JRNL TITL 2 VARIATION IN THE B2A2 LOOP OF MAMMALIAN PRIONS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.2 REMARK 3 NUMBER OF REFLECTIONS : 2612 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 262 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 10.7600 - 1.3200 0.78 1189 133 0.2280 0.2655 REMARK 3 2 1.3200 - 1.0500 0.82 1161 129 0.2119 0.2638 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 2.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 3.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7RVI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1000259066. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : 28-JUN-18 REMARK 240 TEMPERATURE (KELVIN) : 100.0 REMARK 240 PH : 6.50 REMARK 240 NUMBER OF CRYSTALS USED : 1 REMARK 240 MICROSCOPE MODEL : FEI TECNAI F30 REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 300 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 2612 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 240 RESOLUTION RANGE LOW (A) : 10.760 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 79.9 REMARK 240 DATA REDUNDANCY : 8.391 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.05 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.08 REMARK 240 COMPLETENESS FOR SHELL (%) : 83.5 REMARK 240 DATA REDUNDANCY IN SHELL : 8.56 REMARK 240 R MERGE FOR SHELL (I) : 0.58900 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 240 SOFTWARE USED : SHELXD REMARK 240 STARTING MODEL : NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 31.38000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 2.42500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 31.38000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 2.42500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: 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 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 176 O REMARK 620 2 VAL A 176 OXT 53.8 REMARK 620 3 CAC A 201 O2 17.5 71.1 REMARK 620 4 CAC A 201 O1 16.0 69.8 3.7 REMARK 620 N 1 2 3 DBREF 7RVI A 168 176 UNP G5B4V6 G5B4V6_HETGA 158 166 SEQRES 1 A 9 GLN TYR ASN ASN GLN ASN SER PHE VAL HET CAC A 201 5 HET NA A 202 1 HETNAM CAC CACODYLATE ION HETNAM NA SODIUM ION HETSYN CAC DIMETHYLARSINATE FORMUL 2 CAC C2 H6 AS O2 1- FORMUL 3 NA NA 1+ FORMUL 4 HOH *3(H2 O) LINK O VAL A 176 NA NA A 202 1555 3454 2.06 LINK OXT VAL A 176 NA NA A 202 1555 3454 2.53 LINK O2 CAC A 201 NA NA A 202 1555 1555 1.98 LINK O1 CAC A 201 NA NA A 202 1555 1545 2.07 CRYST1 62.760 4.850 21.520 90.00 109.14 90.00 C 1 2 1 4 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 0.015934 0.000000 0.005530 0.00000 SCALE2 0.000000 0.206186 0.000000 0.00000 SCALE3 0.000000 0.000000 0.049187 0.00000 ATOM 1 N GLN A 168 17.842 0.513 22.871 1.00 4.46 N ATOM 2 CA GLN A 168 16.631 -0.238 22.598 1.00 2.31 C ATOM 3 C GLN A 168 16.092 0.196 21.238 1.00 2.11 C ATOM 4 O GLN A 168 16.200 1.361 20.898 1.00 4.13 O ATOM 5 CB GLN A 168 15.611 0.023 23.698 1.00 2.31 C ATOM 6 CG GLN A 168 16.037 -0.549 25.088 1.00 3.97 C ATOM 7 CD GLN A 168 15.235 0.018 26.254 1.00 1.62 C ATOM 8 OE1 GLN A 168 14.924 1.203 26.276 1.00 7.17 O ATOM 9 NE2 GLN A 168 14.876 -0.820 27.209 1.00 4.78 N ATOM 10 N TYR A 169 15.547 -0.739 20.454 1.00 2.99 N ATOM 11 CA TYR A 169 15.101 -0.464 19.084 1.00 1.87 C ATOM 12 C TYR A 169 13.641 -0.897 18.912 1.00 2.35 C ATOM 13 O TYR A 169 13.309 -2.069 19.115 1.00 1.36 O ATOM 14 CB TYR A 169 15.998 -1.173 18.060 1.00 2.29 C ATOM 15 CG TYR A 169 15.552 -1.018 16.600 1.00 3.26 C ATOM 16 CD1 TYR A 169 14.527 -1.812 16.059 1.00 3.02 C ATOM 17 CD2 TYR A 169 16.195 -0.107 15.758 1.00 3.05 C ATOM 18 CE1 TYR A 169 14.139 -1.661 14.718 1.00 2.87 C ATOM 19 CE2 TYR A 169 15.808 0.048 14.422 1.00 4.03 C ATOM 20 CZ TYR A 169 14.784 -0.738 13.915 1.00 3.38 C ATOM 21 OH TYR A 169 14.392 -0.625 12.595 1.00 4.64 O ATOM 22 N ASN A 170 12.772 0.046 18.537 1.00 2.30 N ATOM 23 CA ASN A 170 11.395 -0.281 18.200 1.00 2.30 C ATOM 24 C ASN A 170 11.040 0.318 16.850 1.00 1.45 C ATOM 25 O ASN A 170 11.219 1.522 16.657 1.00 4.86 O ATOM 26 CB ASN A 170 10.422 0.322 19.206 1.00 1.41 C ATOM 27 CG ASN A 170 8.995 0.104 18.808 1.00 1.64 C ATOM 28 OD1 ASN A 170 8.502 -1.036 18.809 1.00 4.30 O ATOM 29 ND2 ASN A 170 8.315 1.176 18.441 1.00 3.45 N ATOM 30 N ASN A 171 10.498 -0.497 15.946 1.00 1.30 N ATOM 31 CA ASN A 171 9.964 -0.016 14.675 1.00 1.51 C ATOM 32 C ASN A 171 8.636 -0.730 14.474 1.00 1.36 C ATOM 33 O ASN A 171 8.624 -1.951 14.295 1.00 3.08 O ATOM 34 CB ASN A 171 10.943 -0.274 13.510 1.00 2.60 C ATOM 35 CG ASN A 171 10.350 0.016 12.122 1.00 2.23 C ATOM 36 OD1 ASN A 171 10.697 -0.669 11.149 1.00 3.16 O ATOM 37 ND2 ASN A 171 9.495 1.028 12.031 1.00 3.65 N ATOM 38 N GLN A 172 7.534 0.017 14.574 1.00 2.22 N ATOM 39 CA GLN A 172 6.193 -0.483 14.296 1.00 0.75 C ATOM 40 C GLN A 172 5.683 0.138 12.995 1.00 1.14 C ATOM 41 O GLN A 172 5.551 1.362 12.893 1.00 3.04 O ATOM 42 CB GLN A 172 5.259 -0.161 15.458 1.00 0.80 C ATOM 43 CG GLN A 172 5.574 -0.903 16.749 1.00 1.80 C ATOM 44 CD GLN A 172 5.027 -0.243 17.970 1.00 1.32 C ATOM 45 OE1 GLN A 172 5.161 0.968 18.134 1.00 3.51 O ATOM 46 NE2 GLN A 172 4.439 -1.030 18.861 1.00 4.73 N ATOM 47 N ASN A 173 5.360 -0.711 12.023 1.00 2.56 N ATOM 48 CA ASN A 173 4.872 -0.253 10.731 1.00 1.60 C ATOM 49 C ASN A 173 3.482 -0.812 10.465 1.00 1.89 C ATOM 50 O ASN A 173 3.237 -2.005 10.676 1.00 4.67 O ATOM 51 CB ASN A 173 5.746 -0.748 9.601 1.00 2.10 C ATOM 52 CG ASN A 173 7.145 -0.230 9.672 1.00 2.38 C ATOM 53 OD1 ASN A 173 7.364 0.949 9.922 1.00 4.45 O ATOM 54 ND2 ASN A 173 8.098 -1.092 9.390 1.00 2.93 N ATOM 55 N SER A 174 2.607 0.042 9.940 1.00 1.44 N ATOM 56 CA SER A 174 1.264 -0.337 9.532 1.00 1.91 C ATOM 57 C SER A 174 0.984 0.207 8.137 1.00 1.83 C ATOM 58 O SER A 174 1.116 1.409 7.892 1.00 4.73 O ATOM 59 CB SER A 174 0.237 0.190 10.528 1.00 2.50 C ATOM 60 OG SER A 174 -1.075 -0.035 10.083 1.00 4.00 O ATOM 61 N PHE A 175 0.578 -0.685 7.240 1.00 2.90 N ATOM 62 CA PHE A 175 0.228 -0.342 5.869 1.00 2.94 C ATOM 63 C PHE A 175 -1.180 -0.848 5.632 1.00 3.22 C ATOM 64 O PHE A 175 -1.427 -2.053 5.740 1.00 7.23 O ATOM 65 CB PHE A 175 1.164 -0.993 4.866 1.00 2.82 C ATOM 66 CG PHE A 175 2.595 -0.647 5.056 1.00 3.63 C ATOM 67 CD1 PHE A 175 3.385 -1.393 5.903 1.00 4.60 C ATOM 68 CD2 PHE A 175 3.154 0.436 4.395 1.00 4.64 C ATOM 69 CE1 PHE A 175 4.703 -1.082 6.082 1.00 4.94 C ATOM 70 CE2 PHE A 175 4.494 0.748 4.555 1.00 4.38 C ATOM 71 CZ PHE A 175 5.265 -0.008 5.405 1.00 5.41 C ATOM 72 N VAL A 176 -2.096 0.067 5.331 1.00 4.71 N ATOM 73 CA VAL A 176 -3.518 -0.212 5.303 1.00 4.08 C ATOM 74 C VAL A 176 -4.130 0.489 4.093 1.00 4.05 C ATOM 75 O VAL A 176 -3.437 1.291 3.450 1.00 7.38 O ATOM 76 CB VAL A 176 -4.173 0.295 6.623 1.00 7.96 C ATOM 77 CG1 VAL A 176 -5.641 -0.004 6.675 1.00 7.18 C ATOM 78 CG2 VAL A 176 -3.484 -0.283 7.825 1.00 8.53 C ATOM 79 OXT VAL A 176 -5.297 0.318 3.742 1.00 5.43 O TER 80 VAL A 176 HETATM 81 AS CAC A 201 20.304 -2.789 20.224 1.00 12.92 AS HETATM 82 O1 CAC A 201 20.928 -3.940 21.359 1.00 8.76 O HETATM 83 O2 CAC A 201 19.123 -1.728 20.913 1.00 11.70 O HETATM 84 C1 CAC A 201 19.410 -3.708 18.737 1.00 8.84 C HETATM 85 C2 CAC A 201 21.808 -1.781 19.463 1.00 10.88 C HETATM 86 NA NA A 202 19.650 -0.413 22.300 1.00 3.69 NA HETATM 87 O HOH A 301 12.858 -2.431 11.575 1.00 6.19 O HETATM 88 O HOH A 302 -1.881 2.328 8.993 1.00 11.78 O HETATM 89 O HOH A 303 -0.756 1.141 2.581 1.00 9.05 O CONECT 81 82 83 84 85 CONECT 82 81 CONECT 83 81 86 CONECT 84 81 CONECT 85 81 CONECT 86 83 MASTER 173 0 2 0 0 0 0 6 88 1 6 1 END