HEADER RNA BINDING PROTEIN 12-JAN-19 6J60
TITLE HNRNP A1 REVERSIBLE AMYLOID CORE GFGGNDNFG (RESIDUES 209-217)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 9-MER PEPTIDE (GFGGNDNFG) FROM HETEROGENEOUS NUCLEAR
COMPND 3 RIBONUCLEOPROTEIN A1;
COMPND 4 CHAIN: A;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 4 ORGANISM_TAXID: 9606
KEYWDS PHASE SEPARATION, REVERSIBILITY, RNA BINDING PROTEIN, MICROED
EXPDTA ELECTRON CRYSTALLOGRAPHY
AUTHOR F.LUO,H.ZHOU,X.GUI,D.LI,X.LI,C.LIU
REVDAT 3 27-MAR-24 6J60 1 REMARK
REVDAT 2 16-OCT-19 6J60 1 JRNL
REVDAT 1 03-APR-19 6J60 0
JRNL AUTH X.GUI,F.LUO,Y.LI,H.ZHOU,Z.QIN,Z.LIU,J.GU,M.XIE,K.ZHAO,B.DAI,
JRNL AUTH 2 W.S.SHIN,J.HE,L.HE,L.JIANG,M.ZHAO,B.SUN,X.LI,C.LIU,D.LI
JRNL TITL STRUCTURAL BASIS FOR REVERSIBLE AMYLOIDS OF HNRNPA1
JRNL TITL 2 ELUCIDATES THEIR ROLE IN STRESS GRANULE ASSEMBLY.
JRNL REF NAT COMMUN V. 10 2006 2019
JRNL REFN ESSN 2041-1723
JRNL PMID 31043593
JRNL DOI 10.1038/S41467-019-09902-7
REMARK 2
REMARK 2 RESOLUTION. 0.96 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.10_2155: ???)
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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.96
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 3.97
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 86.9
REMARK 3 NUMBER OF REFLECTIONS : 5150
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.235
REMARK 3 R VALUE (WORKING SET) : 0.233
REMARK 3 FREE R VALUE : 0.248
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.120
REMARK 3 FREE R VALUE TEST SET COUNT : 521
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
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) : 0.170
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.520
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
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 : 0.014 64
REMARK 3 ANGLE : 1.044 84
REMARK 3 CHIRALITY : 0.122 5
REMARK 3 PLANARITY : 0.006 14
REMARK 3 DIHEDRAL : 10.981 19
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: PHENIX.REFINE
REMARK 4
REMARK 4 6J60 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JAN-19.
REMARK 100 THE DEPOSITION ID IS D_1300010533.
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 : NULL
REMARK 240 TEMPERATURE (KELVIN) : NULL
REMARK 240 PH : NULL
REMARK 240 NUMBER OF CRYSTALS USED : NULL
REMARK 240 MICROSCOPE MODEL : FEI TECNAI F20
REMARK 240 DETECTOR TYPE : GATAN ULTRASCAN 4000 (4K X 4K)
REMARK 240 ACCELERATION VOLTAGE (KV) : 200
REMARK 240 NUMBER OF UNIQUE REFLECTIONS : NULL
REMARK 240 RESOLUTION RANGE HIGH (A) : NULL
REMARK 240 RESOLUTION RANGE LOW (A) : NULL
REMARK 240 DATA SCALING SOFTWARE : NULL
REMARK 240 COMPLETENESS FOR RANGE (%) : NULL
REMARK 240 DATA REDUNDANCY : NULL
REMARK 240 IN THE HIGHEST RESOLUTION SHELL
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :NULL
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :NULL
REMARK 240 COMPLETENESS FOR SHELL (%) : NULL
REMARK 240 DATA REDUNDANCY IN SHELL : NULL
REMARK 240 R MERGE FOR SHELL (I) : NULL
REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 240 SOFTWARE USED : NULL
REMARK 240 STARTING MODEL : NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
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 2.50500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.22500
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.90000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 18.22500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 2.50500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 13.90000
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
DBREF 6J60 A 209 217 PDB 6J60 6J60 209 217
SEQRES 1 A 9 GLY PHE GLY GLY ASN ASP ASN PHE GLY
FORMUL 2 HOH *4(H2 O)
CRYST1 5.010 27.800 36.450 90.00 90.00 90.00 P 21 21 21 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 0.199601 0.000000 0.000000 0.00000
SCALE2 0.000000 0.035971 0.000000 0.00000
SCALE3 0.000000 0.000000 0.027435 0.00000
ATOM 1 N GLY A 209 1.299 9.333 7.766 1.00 6.34 N
ATOM 2 CA GLY A 209 1.226 9.520 9.201 1.00 7.74 C
ATOM 3 C GLY A 209 2.254 8.775 10.046 1.00 5.21 C
ATOM 4 O GLY A 209 3.084 8.034 9.513 1.00 5.06 O
ATOM 5 HA2 GLY A 209 1.322 10.466 9.393 1.00 9.29 H
ATOM 6 HA3 GLY A 209 0.346 9.246 9.503 1.00 9.29 H
ATOM 7 N PHE A 210 2.178 8.969 11.369 1.00 5.20 N
ATOM 8 CA PHE A 210 3.038 8.259 12.318 1.00 4.08 C
ATOM 9 C PHE A 210 2.908 6.758 12.059 1.00 4.84 C
ATOM 10 O PHE A 210 1.793 6.228 11.974 1.00 6.53 O
ATOM 11 CB PHE A 210 2.579 8.606 13.765 1.00 5.13 C
ATOM 12 CG PHE A 210 3.406 7.962 14.866 1.00 4.23 C
ATOM 13 CD1 PHE A 210 3.204 6.641 15.209 1.00 4.05 C
ATOM 14 CD2 PHE A 210 4.383 8.687 15.556 1.00 5.65 C
ATOM 15 CE1 PHE A 210 3.996 6.036 16.183 1.00 4.62 C
ATOM 16 CE2 PHE A 210 5.170 8.085 16.540 1.00 5.17 C
ATOM 17 CZ PHE A 210 4.971 6.774 16.849 1.00 4.86 C
ATOM 18 H PHE A 210 1.629 9.515 11.743 1.00 6.24 H
ATOM 19 HA PHE A 210 3.963 8.527 12.201 1.00 4.89 H
ATOM 20 HB2 PHE A 210 2.631 9.567 13.884 1.00 6.15 H
ATOM 21 HB3 PHE A 210 1.662 8.312 13.878 1.00 6.15 H
ATOM 22 HD1 PHE A 210 2.567 6.138 14.753 1.00 4.87 H
ATOM 23 HD2 PHE A 210 4.533 9.577 15.332 1.00 6.78 H
ATOM 24 HE1 PHE A 210 3.855 5.144 16.407 1.00 5.54 H
ATOM 25 HE2 PHE A 210 5.819 8.578 16.987 1.00 6.21 H
ATOM 26 HZ PHE A 210 5.480 6.374 17.517 1.00 5.84 H
ATOM 27 N GLY A 211 4.057 6.074 11.901 1.00 4.15 N
ATOM 28 CA GLY A 211 4.063 4.655 11.602 1.00 5.49 C
ATOM 29 C GLY A 211 3.817 4.304 10.145 1.00 5.27 C
ATOM 30 O GLY A 211 3.770 3.117 9.802 1.00 9.58 O
ATOM 31 H GLY A 211 4.841 6.422 11.964 1.00 4.99 H
ATOM 32 HA2 GLY A 211 4.922 4.284 11.857 1.00 6.59 H
ATOM 33 HA3 GLY A 211 3.378 4.219 12.133 1.00 6.59 H
ATOM 34 N GLY A 212 3.676 5.301 9.278 1.00 5.48 N
ATOM 35 CA GLY A 212 3.359 5.124 7.872 1.00 4.54 C
ATOM 36 C GLY A 212 4.088 6.112 6.979 1.00 3.41 C
ATOM 37 O GLY A 212 5.250 6.443 7.260 1.00 5.40 O
ATOM 38 H GLY A 212 3.765 6.128 9.496 1.00 6.57 H
ATOM 39 HA2 GLY A 212 3.602 4.226 7.597 1.00 5.45 H
ATOM 40 HA3 GLY A 212 2.405 5.238 7.740 1.00 5.45 H
ATOM 41 N ASN A 213 3.459 6.560 5.885 1.00 3.03 N
ATOM 42 CA ASN A 213 4.153 7.340 4.850 1.00 3.99 C
ATOM 43 C ASN A 213 3.507 8.710 4.626 1.00 3.53 C
ATOM 44 O ASN A 213 2.287 8.879 4.773 1.00 4.17 O
ATOM 45 CB ASN A 213 4.169 6.581 3.509 1.00 5.11 C
ATOM 46 CG ASN A 213 4.749 5.200 3.645 1.00 6.10 C
ATOM 47 OD1 ASN A 213 5.958 5.046 3.802 1.00 6.66 O
ATOM 48 ND2 ASN A 213 3.890 4.185 3.637 1.00 7.27 N
ATOM 49 H ASN A 213 2.627 6.424 5.718 1.00 3.63 H
ATOM 50 HA ASN A 213 5.072 7.483 5.125 1.00 4.79 H
ATOM 51 HB2 ASN A 213 3.260 6.495 3.181 1.00 6.13 H
ATOM 52 HB3 ASN A 213 4.709 7.074 2.871 1.00 6.13 H
ATOM 53 HD21 ASN A 213 4.177 3.378 3.712 1.00 8.72 H
ATOM 54 HD22 ASN A 213 3.047 4.336 3.556 1.00 8.72 H
ATOM 55 N ASP A 214 4.358 9.670 4.223 1.00 4.80 N
ATOM 56 CA ASP A 214 3.958 11.027 3.846 1.00 4.36 C
ATOM 57 C ASP A 214 4.581 11.359 2.476 1.00 3.19 C
ATOM 58 O ASP A 214 5.813 11.414 2.339 1.00 3.80 O
ATOM 59 CB ASP A 214 4.353 12.027 4.941 1.00 9.87 C
ATOM 60 CG ASP A 214 3.631 11.761 6.292 1.00 10.41 C
ATOM 61 OD1 ASP A 214 4.094 10.909 7.082 1.00 12.48 O
ATOM 62 OD2 ASP A 214 2.588 12.397 6.561 1.00 16.66 O
ATOM 63 H ASP A 214 5.206 9.546 4.161 1.00 5.76 H
ATOM 64 HA ASP A 214 2.993 11.056 3.750 1.00 5.24 H
ATOM 65 HB2 ASP A 214 5.308 11.967 5.094 1.00 11.85 H
ATOM 66 HB3 ASP A 214 4.120 12.923 4.649 1.00 11.85 H
ATOM 67 N ASN A 215 3.716 11.537 1.453 1.00 2.88 N
ATOM 68 CA ASN A 215 4.106 11.647 0.040 1.00 2.64 C
ATOM 69 C ASN A 215 3.682 13.014 -0.500 1.00 2.74 C
ATOM 70 O ASN A 215 2.486 13.348 -0.485 1.00 3.48 O
ATOM 71 CB ASN A 215 3.404 10.536 -0.778 1.00 4.49 C
ATOM 72 CG ASN A 215 3.817 9.134 -0.341 1.00 3.05 C
ATOM 73 OD1 ASN A 215 5.018 8.785 -0.312 1.00 3.85 O
ATOM 74 ND2 ASN A 215 2.825 8.326 0.035 1.00 5.92 N
ATOM 75 H ASN A 215 2.866 11.599 1.566 1.00 3.46 H
ATOM 76 HA ASN A 215 5.067 11.552 -0.052 1.00 3.17 H
ATOM 77 HB2 ASN A 215 2.444 10.617 -0.661 1.00 5.39 H
ATOM 78 HB3 ASN A 215 3.634 10.639 -1.714 1.00 5.39 H
ATOM 79 HD21 ASN A 215 2.997 7.523 0.292 1.00 7.10 H
ATOM 80 HD22 ASN A 215 2.012 8.607 0.021 1.00 7.10 H
ATOM 81 N PHE A 216 4.657 13.798 -0.987 1.00 4.64 N
ATOM 82 CA PHE A 216 4.419 15.120 -1.574 1.00 5.57 C
ATOM 83 C PHE A 216 4.837 15.124 -3.054 1.00 5.56 C
ATOM 84 O PHE A 216 6.024 14.958 -3.367 1.00 7.88 O
ATOM 85 CB PHE A 216 5.158 16.214 -0.761 1.00 5.52 C
ATOM 86 CG PHE A 216 4.856 16.188 0.761 1.00 5.82 C
ATOM 87 CD1 PHE A 216 5.580 15.363 1.622 1.00 5.57 C
ATOM 88 CD2 PHE A 216 3.834 16.983 1.318 1.00 8.02 C
ATOM 89 CE1 PHE A 216 5.312 15.329 2.976 1.00 8.90 C
ATOM 90 CE2 PHE A 216 3.562 16.945 2.693 1.00 7.38 C
ATOM 91 CZ PHE A 216 4.280 16.119 3.519 1.00 8.55 C
ATOM 92 H PHE A 216 5.487 13.575 -0.986 1.00 5.57 H
ATOM 93 HA PHE A 216 3.469 15.313 -1.534 1.00 6.69 H
ATOM 94 HB2 PHE A 216 6.114 16.093 -0.875 1.00 6.62 H
ATOM 95 HB3 PHE A 216 4.895 17.084 -1.100 1.00 6.62 H
ATOM 96 HD1 PHE A 216 6.257 14.827 1.277 1.00 6.69 H
ATOM 97 HD2 PHE A 216 3.333 17.539 0.766 1.00 9.62 H
ATOM 98 HE1 PHE A 216 5.806 14.770 3.530 1.00 10.68 H
ATOM 99 HE2 PHE A 216 2.883 17.474 3.045 1.00 8.85 H
ATOM 100 HZ PHE A 216 4.105 16.100 4.432 1.00 10.26 H
ATOM 101 N GLY A 217 3.867 15.332 -3.959 1.00 6.84 N
ATOM 102 CA GLY A 217 4.095 15.330 -5.400 1.00 8.12 C
ATOM 103 C GLY A 217 3.097 16.166 -6.209 1.00 9.32 C
ATOM 104 O GLY A 217 2.283 16.921 -5.689 1.00 6.88 O
ATOM 105 OXT GLY A 217 3.073 16.131 -7.441 0.65 12.68 O
ATOM 106 H GLY A 217 3.047 15.479 -3.748 1.00 8.21 H
ATOM 107 HA2 GLY A 217 4.985 15.672 -5.578 1.00 9.74 H
ATOM 108 HA3 GLY A 217 4.054 14.417 -5.724 1.00 9.74 H
TER 109 GLY A 217
HETATM 110 O HOH A 301 6.800 12.645 -4.669 1.00 20.37 O
HETATM 111 O HOH A 302 5.298 14.789 -8.582 1.00 16.27 O
HETATM 112 O HOH A 303 4.741 0.478 10.919 1.00 21.42 O
HETATM 113 O HOH A 304 6.599 2.208 5.379 1.00 19.02 O
MASTER 158 0 0 0 0 0 0 6 67 1 0 1
END