HEADER IMMUNE SYSTEM 25-JUL-25 9PSE TITLE IN SITU MICROED STRUCTURE OF IL-5 ACTIVATED HUMAN EOSINOPHIL MAJOR TITLE 2 BASIC PROTEIN-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BONE MARROW PROTEOGLYCAN; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: BMPG,PROTEOGLYCAN 2; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: HUMAN MBP-1 DERIVES FROM A PRECURSOR OR PROFORM PROMBP COMPND 7 CODED BY GENE PRG2 IN EOSINOPHILS. PROTEIN MBP-1 NATURALLY FORMS COMPND 8 INTRAGRANULAR NANOCRYSTALS THAT GET DISASSEMBLED UPON ACTIVATION, COMPND 9 INCLUDING CYTOKINE IL-5. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PRG2, MBP; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS EFFECTOR, NANOCRYSTAL, IN-SITU, INTRACELLULAR, IMMUNE SYSTEM EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR J.E.YANG,C.A.BINGMAN,J.MITCHELL,D.MOSHER,E.R.WRIGHT REVDAT 1 03-SEP-25 9PSE 0 JRNL AUTH J.E.YANG,C.A.BINGMAN,J.MITCHELL,D.MOSHER,E.R.WRIGHT JRNL TITL IN SITU MICROED STRUCTURE OF THE EOSINOPHIL MAJOR BASIC JRNL TITL 2 PROTEIN-1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 3.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 3 NUMBER OF REFLECTIONS : 3496 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.282 REMARK 3 R VALUE (WORKING SET) : 0.278 REMARK 3 FREE R VALUE : 0.320 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.380 REMARK 3 FREE R VALUE TEST SET COUNT : 363 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 30.1900 - 4.3300 0.97 1193 153 0.2497 0.3003 REMARK 3 2 4.3200 - 3.4300 0.89 1092 117 0.2902 0.3183 REMARK 3 3 3.4300 - 3.0000 0.69 848 93 0.3305 0.3834 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.578 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.249 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.00 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 : 0.002 1990 REMARK 3 ANGLE : 0.424 2692 REMARK 3 CHIRALITY : 0.039 258 REMARK 3 PLANARITY : 0.006 344 REMARK 3 DIHEDRAL : 12.188 698 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 9PSE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1000298294. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : CELL 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 : TFS KRIOS REMARK 240 DETECTOR TYPE : FEI CETA (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 300 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 6805 REMARK 240 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 240 RESOLUTION RANGE LOW (A) : 30.690 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 85.7 REMARK 240 DATA REDUNDANCY : NULL REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :3.00 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :3.44 REMARK 240 COMPLETENESS FOR SHELL (%) : NULL REMARK 240 DATA REDUNDANCY IN SHELL : NULL REMARK 240 R MERGE FOR SHELL (I) : 1.37600 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 240 SOFTWARE USED : PHENIX REMARK 240 STARTING MODEL : NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 28.90000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH1 ARG A 127 OD1 ASN A 140 2656 2.14 REMARK 500 OH TYR B 184 OH TYR A 184 2656 2.19 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 SER B 166 93.11 -66.58 REMARK 500 PRO B 190 61.70 -111.27 REMARK 500 THR A 117 173.46 -57.91 REMARK 500 SER A 166 -141.16 -104.05 REMARK 500 CYS A 169 42.52 -144.52 REMARK 500 GLN A 173 135.65 -171.52 REMARK 500 SER A 178 -170.07 -67.29 REMARK 500 TYR A 184 59.33 -113.98 REMARK 500 PRO A 190 61.70 -117.89 REMARK 500 SER A 192 -34.73 77.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 AUTHORS STATE THAT THE CHLORIDE IONS A301 AND B301 MODELED COULD BE REMARK 600 BROMIDE IONS. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9PPV RELATED DB: PDB REMARK 900 STRUCTURE DETERMINED FROM NON-ACTIVATED EOSINOPHILS REMARK 900 RELATED ID: 9PSK RELATED DB: PDB REMARK 900 STRUCTURE DETERMINED FROM IL-33-ACTIVATED EOSINOPHILS DBREF 9PSE B 107 222 UNP P13727 PRG2_HUMAN 107 222 DBREF 9PSE A 107 222 UNP P13727 PRG2_HUMAN 107 222 SEQRES 1 B 116 CYS ARG TYR LEU LEU VAL ARG SER LEU GLN THR PHE SER SEQRES 2 B 116 GLN ALA TRP PHE THR CYS ARG ARG CYS TYR ARG GLY ASN SEQRES 3 B 116 LEU VAL SER ILE HIS ASN PHE ASN ILE ASN TYR ARG ILE SEQRES 4 B 116 GLN CYS SER VAL SER ALA LEU ASN GLN GLY GLN VAL TRP SEQRES 5 B 116 ILE GLY GLY ARG ILE THR GLY SER GLY ARG CYS ARG ARG SEQRES 6 B 116 PHE GLN TRP VAL ASP GLY SER ARG TRP ASN PHE ALA TYR SEQRES 7 B 116 TRP ALA ALA HIS GLN PRO TRP SER ARG GLY GLY HIS CYS SEQRES 8 B 116 VAL ALA LEU CYS THR ARG GLY GLY HIS TRP ARG ARG ALA SEQRES 9 B 116 HIS CYS LEU ARG ARG LEU PRO PHE ILE CYS SER TYR SEQRES 1 A 116 CYS ARG TYR LEU LEU VAL ARG SER LEU GLN THR PHE SER SEQRES 2 A 116 GLN ALA TRP PHE THR CYS ARG ARG CYS TYR ARG GLY ASN SEQRES 3 A 116 LEU VAL SER ILE HIS ASN PHE ASN ILE ASN TYR ARG ILE SEQRES 4 A 116 GLN CYS SER VAL SER ALA LEU ASN GLN GLY GLN VAL TRP SEQRES 5 A 116 ILE GLY GLY ARG ILE THR GLY SER GLY ARG CYS ARG ARG SEQRES 6 A 116 PHE GLN TRP VAL ASP GLY SER ARG TRP ASN PHE ALA TYR SEQRES 7 A 116 TRP ALA ALA HIS GLN PRO TRP SER ARG GLY GLY HIS CYS SEQRES 8 A 116 VAL ALA LEU CYS THR ARG GLY GLY HIS TRP ARG ARG ALA SEQRES 9 A 116 HIS CYS LEU ARG ARG LEU PRO PHE ILE CYS SER TYR HET CL B 301 1 HET CL A 301 1 HETNAM CL CHLORIDE ION FORMUL 3 CL 2(CL 1-) FORMUL 5 HOH *3(H2 O) HELIX 1 AA1 THR B 117 ARG B 130 1 14 HELIX 2 AA2 ASN B 138 VAL B 149 1 12 HELIX 3 AA3 THR A 117 CYS A 128 1 12 HELIX 4 AA4 ASN A 138 VAL A 149 1 12 SHEET 1 AA1 3 TYR B 109 GLN B 116 0 SHEET 2 AA1 3 LEU B 216 SER B 221 -1 O CYS B 220 N LEU B 110 SHEET 3 AA1 3 ASN B 132 LEU B 133 -1 N ASN B 132 O SER B 221 SHEET 1 AA2 4 PHE B 172 TRP B 174 0 SHEET 2 AA2 4 GLN B 156 ILE B 163 -1 O ARG B 162 N GLN B 173 SHEET 3 AA2 4 CYS B 197 CYS B 201 -1 O LEU B 200 N VAL B 157 SHEET 4 AA2 4 TRP B 207 ALA B 210 -1 O ALA B 210 N CYS B 197 SHEET 1 AA3 3 ARG A 108 GLN A 116 0 SHEET 2 AA3 3 LEU A 216 TYR A 222 -1 O CYS A 220 N LEU A 110 SHEET 3 AA3 3 ASN A 132 LEU A 133 -1 N ASN A 132 O SER A 221 SHEET 1 AA4 4 ARG A 171 TRP A 174 0 SHEET 2 AA4 4 GLN A 156 THR A 164 -1 N THR A 164 O ARG A 171 SHEET 3 AA4 4 CYS A 197 CYS A 201 -1 O LEU A 200 N VAL A 157 SHEET 4 AA4 4 TRP A 207 ALA A 210 -1 O ALA A 210 N CYS A 197 SSBOND 1 CYS B 125 CYS B 220 1555 1555 2.03 SSBOND 2 CYS B 197 CYS B 212 1555 1555 2.03 SSBOND 3 CYS A 125 CYS A 220 1555 1555 2.03 SSBOND 4 CYS A 197 CYS A 212 1555 1555 2.03 CISPEP 1 GLN B 189 PRO B 190 0 -6.56 CISPEP 2 GLN A 189 PRO A 190 0 -11.32 CRYST1 30.200 57.800 58.600 90.00 91.20 90.00 P 1 21 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 0.033113 0.000000 0.000694 0.00000 SCALE2 0.000000 0.017301 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017069 0.00000 TER 1890 TYR B 222 TER 3780 TYR A 222 HETATM 3781 CL CL B 301 25.691 -0.863 49.176 1.00 40.05 CL HETATM 3782 CL CL A 301 1.853 19.634 19.897 1.00 39.80 CL HETATM 3783 O HOH B 401 29.989 2.898 42.266 1.00 39.36 O HETATM 3784 O HOH B 402 31.325 14.517 44.261 1.00 38.99 O HETATM 3785 O HOH A 401 -4.159 13.853 14.590 1.00 38.96 O CONECT 317 1852 CONECT 1469 1703 CONECT 1703 1469 CONECT 1852 317 CONECT 2207 3742 CONECT 3359 3593 CONECT 3593 3359 CONECT 3742 2207 MASTER 222 0 2 4 14 0 0 6 1933 2 8 18 END