HEADER PROTEIN TRANSPORT 26-NOV-24 9EIU TITLE CRYSTAL STRUCTURE OF THE HUMAN CAVIN1 HR1 TS/DD MUTANT DOMAIN BOUND TO TITLE 2 NANOBODY B7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAVEOLAE-ASSOCIATED PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CAVIN-1,POLYMERASE I AND TRANSCRIPT RELEASE FACTOR; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NANOBODY B7; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CAVIN1, PTRF, FKSG13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 10 ORGANISM_TAXID: 30538; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CAVEOLAE, CAVIN1, NANOBODY, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR B.M.COLLINS,Y.GAO REVDAT 1 26-FEB-25 9EIU 0 JRNL AUTH B.M.COLLINS,Y.GAO JRNL TITL CRYSTAL STRUCTURE OF THE HUMAN CAVIN1 HR1 DOMAIN BOUND TO JRNL TITL 2 NANOBODY B7 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 4.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 4.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.060 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 1975 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.580 REMARK 3 FREE R VALUE TEST SET COUNT : 130 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 30.6500 - 4.0000 0.99 1845 130 0.2025 0.2635 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) : 0.000 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.187 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 94.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 183.0 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 : 0.004 1226 REMARK 3 ANGLE : 0.786 1657 REMARK 3 CHIRALITY : 0.049 188 REMARK 3 PLANARITY : 0.010 217 REMARK 3 DIHEDRAL : 14.535 452 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 9EIU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1000290364. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1975 REMARK 200 RESOLUTION RANGE HIGH (A) : 4.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.50 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM THIOCYANATE, 20% PEG REMARK 280 3350 AND 0.2 M POTASSIUM CITRATE, 20% PEG 3350, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 GLY A 39 REMARK 465 SER A 40 REMARK 465 PRO A 41 REMARK 465 GLY A 42 REMARK 465 ILE A 43 REMARK 465 GLN A 44 REMARK 465 LEU A 45 REMARK 465 ILE A 46 REMARK 465 LYS A 47 REMARK 465 SER A 48 REMARK 465 ASP A 49 REMARK 465 GLN A 50 REMARK 465 VAL A 51 REMARK 465 ASN A 52 REMARK 465 GLY A 53 REMARK 465 VAL A 54 REMARK 465 LEU A 55 REMARK 465 VAL A 56 REMARK 465 GLY A 99 REMARK 465 LYS A 100 REMARK 465 ALA A 101 REMARK 465 HIS A 102 REMARK 465 ALA A 103 REMARK 465 THR A 104 REMARK 465 ASP A 105 REMARK 465 ASP A 106 REMARK 465 ASN A 107 REMARK 465 THR A 108 REMARK 465 VAL A 109 REMARK 465 SER A 110 REMARK 465 LYS A 111 REMARK 465 LEU A 112 REMARK 465 LEU A 113 REMARK 465 GLU A 114 REMARK 465 LYS A 115 REMARK 465 VAL A 116 REMARK 465 ARG A 117 REMARK 465 LYS A 118 REMARK 465 VAL A 119 REMARK 465 SER A 120 REMARK 465 VAL A 121 REMARK 465 ASN A 122 REMARK 465 VAL A 123 REMARK 465 LYS A 124 REMARK 465 THR A 125 REMARK 465 VAL A 126 REMARK 465 ARG A 127 REMARK 465 GLY A 128 REMARK 465 SER A 129 REMARK 465 LEU A 130 REMARK 465 GLU A 131 REMARK 465 ARG A 132 REMARK 465 GLN A 133 REMARK 465 ALA A 134 REMARK 465 GLY A 135 REMARK 465 GLN A 136 REMARK 465 ILE A 137 REMARK 465 LYS A 138 REMARK 465 LYS A 139 REMARK 465 LEU A 140 REMARK 465 GLU A 141 REMARK 465 VAL A 142 REMARK 465 ASN A 143 REMARK 465 GLU A 144 REMARK 465 ALA A 145 REMARK 465 GLU A 146 REMARK 465 LEU A 147 REMARK 465 LEU A 148 REMARK 465 ARG A 149 REMARK 465 ARG A 150 REMARK 465 ARG A 151 REMARK 465 ASN A 152 REMARK 465 PHE A 153 REMARK 465 LYS A 154 REMARK 465 HIS B 117 REMARK 465 HIS B 118 REMARK 465 HIS B 119 REMARK 465 HIS B 120 REMARK 465 HIS B 121 REMARK 465 HIS B 122 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 LYS B 65 61.16 35.24 REMARK 500 REMARK 500 REMARK: NULL DBREF 9EIU A 45 154 UNP Q6NZI2 CAVN1_HUMAN 43 152 DBREF 9EIU B 2 122 PDB 9EIU 9EIU 2 122 SEQADV 9EIU GLY A 39 UNP Q6NZI2 EXPRESSION TAG SEQADV 9EIU SER A 40 UNP Q6NZI2 EXPRESSION TAG SEQADV 9EIU PRO A 41 UNP Q6NZI2 EXPRESSION TAG SEQADV 9EIU GLY A 42 UNP Q6NZI2 EXPRESSION TAG SEQADV 9EIU ILE A 43 UNP Q6NZI2 EXPRESSION TAG SEQADV 9EIU GLN A 44 UNP Q6NZI2 EXPRESSION TAG SEQADV 9EIU ASP A 105 UNP Q6NZI2 THR 103 ENGINEERED MUTATION SEQADV 9EIU ASP A 106 UNP Q6NZI2 SER 104 ENGINEERED MUTATION SEQRES 1 A 116 GLY SER PRO GLY ILE GLN LEU ILE LYS SER ASP GLN VAL SEQRES 2 A 116 ASN GLY VAL LEU VAL LEU SER LEU LEU ASP LYS ILE ILE SEQRES 3 A 116 GLY ALA VAL ASP GLN ILE GLN LEU THR GLN ALA GLN LEU SEQRES 4 A 116 GLU GLU ARG GLN ALA GLU MET GLU GLY ALA VAL GLN SER SEQRES 5 A 116 ILE GLN GLY GLU LEU SER LYS LEU GLY LYS ALA HIS ALA SEQRES 6 A 116 THR ASP ASP ASN THR VAL SER LYS LEU LEU GLU LYS VAL SEQRES 7 A 116 ARG LYS VAL SER VAL ASN VAL LYS THR VAL ARG GLY SER SEQRES 8 A 116 LEU GLU ARG GLN ALA GLY GLN ILE LYS LYS LEU GLU VAL SEQRES 9 A 116 ASN GLU ALA GLU LEU LEU ARG ARG ARG ASN PHE LYS SEQRES 1 B 121 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 121 ALA GLY GLY SER LEU ARG LEU SER CYS ALA VAL SER GLY SEQRES 3 B 121 ILE ARG VAL ASN VAL ASN ALA MET TYR TRP TYR ARG GLN SEQRES 4 B 121 ALA PRO GLY LYS GLN ARG GLU LEU VAL ALA ILE ILE THR SEQRES 5 B 121 THR PHE GLY SER THR ASN TYR ALA ASP SER ALA LYS GLY SEQRES 6 B 121 ARG PHE THR ILE SER ARG ASP ASN THR LYS ASN THR VAL SEQRES 7 B 121 TYR LEU GLN MET ASP ASN LEU LYS PRO GLU ASP THR ALA SEQRES 8 B 121 VAL TYR TYR CYS ASN ALA PRO GLN PHE THR ASP ARG TYR SEQRES 9 B 121 TRP GLY GLN GLY THR GLN VAL THR VAL SER SER HIS HIS SEQRES 10 B 121 HIS HIS HIS HIS HELIX 1 AA1 SER A 58 LYS A 97 1 40 HELIX 2 AA2 LYS B 87 THR B 91 5 5 HELIX 3 AA3 ALA B 98 THR B 102 5 5 SHEET 1 AA1 4 GLN B 4 SER B 8 0 SHEET 2 AA1 4 LEU B 19 SER B 26 -1 O SER B 22 N SER B 8 SHEET 3 AA1 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 19 SHEET 4 AA1 4 PHE B 68 ASP B 73 -1 N SER B 71 O TYR B 80 SHEET 1 AA2 6 GLY B 11 GLN B 14 0 SHEET 2 AA2 6 THR B 110 SER B 115 1 O THR B 113 N GLY B 11 SHEET 3 AA2 6 ALA B 92 ASN B 97 -1 N ALA B 92 O VAL B 112 SHEET 4 AA2 6 MET B 35 GLN B 40 -1 N TYR B 36 O ASN B 97 SHEET 5 AA2 6 GLU B 47 ILE B 52 -1 O GLU B 47 N ARG B 39 SHEET 6 AA2 6 THR B 58 TYR B 60 -1 O ASN B 59 N ILE B 51 CRYST1 58.669 58.669 61.293 90.00 90.00 120.00 P 3 3 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 0.017045 0.009841 0.000000 0.00000 SCALE2 0.000000 0.019682 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016315 0.00000