HEADER CELL CYCLE 01-FEB-23 8G0P TITLE CRYSTAL STRUCTURE OF THE HUMAN NDC80:NUF2 LOOP REGION COMPND MOL_ID: 1; COMPND 2 MOLECULE: KINETOCHORE PROTEIN NDC80 HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HIGHLY EXPRESSED IN CANCER PROTEIN,KINETOCHORE PROTEIN HEC1, COMPND 5 HSHEC1,KINETOCHORE-ASSOCIATED PROTEIN 2,RETINOBLASTOMA-ASSOCIATED COMPND 6 PROTEIN HEC; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: KINETOCHORE PROTEIN NUF2; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: HNUF2,HNUF2R,HSNUF2,CELL DIVISION CYCLE-ASSOCIATED PROTEIN COMPND 12 1; COMPND 13 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: NDC80, HEC, HEC1, KNTC2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: NUF2, CDCA1, NUF2R; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CELL DIVISION, CHROMOSOME SEGREGATION, KINETOCHORE, NDC80 COMPLEX, KEYWDS 2 NDC80, NUF2, LOOP, HINGE, HUMAN, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.ZAHM,S.JENNI,S.C.HARRISON REVDAT 1 29-MAR-23 8G0P 0 JRNL AUTH J.A.ZAHM,S.JENNI,S.C.HARRISON JRNL TITL STRUCTURE OF THE NDC80 COMPLEX AND ITS INTERACTIONS AT THE JRNL TITL 2 YEAST KINETOCHORE-MICROTUBULE INTERFACE. JRNL REF OPEN BIOLOGY V. 13 20378 2023 JRNL REFN ESSN 2046-2441 JRNL PMID 36883282 JRNL DOI 10.1098/RSOB.220378 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 36742 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.262 REMARK 3 R VALUE (WORKING SET) : 0.260 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1836 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 40.7500 - 4.7000 0.99 2705 148 0.2266 0.2757 REMARK 3 2 4.7000 - 3.7300 1.00 2741 127 0.2010 0.2109 REMARK 3 3 3.7300 - 3.2600 0.99 2704 139 0.2515 0.3012 REMARK 3 4 3.2600 - 2.9600 0.99 2740 111 0.2709 0.2778 REMARK 3 5 2.9600 - 2.7500 0.99 2686 142 0.2560 0.3520 REMARK 3 6 2.7500 - 2.5900 1.00 2712 151 0.2888 0.3623 REMARK 3 7 2.5900 - 2.4600 0.99 2763 123 0.2836 0.3310 REMARK 3 8 2.4600 - 2.3500 0.99 2716 155 0.3010 0.3309 REMARK 3 9 2.3500 - 2.2600 0.98 2655 164 0.3297 0.3701 REMARK 3 10 2.2600 - 2.1800 0.99 2664 139 0.3819 0.4039 REMARK 3 11 2.1800 - 2.1100 0.99 2723 178 0.4476 0.4289 REMARK 3 12 2.1100 - 2.0500 0.98 2657 131 0.4823 0.4424 REMARK 3 13 2.0500 - 2.0000 0.91 2440 128 0.5149 0.4990 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) : 0.308 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.472 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.66 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 : 0.003 1995 REMARK 3 ANGLE : 0.456 2668 REMARK 3 CHIRALITY : 0.028 297 REMARK 3 PLANARITY : 0.003 346 REMARK 3 DIHEDRAL : 3.600 260 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -15.5161 3.2093 29.4259 REMARK 3 T TENSOR REMARK 3 T11: 0.6739 T22: 0.6879 REMARK 3 T33: 0.5584 T12: 0.0321 REMARK 3 T13: 0.0158 T23: -0.0450 REMARK 3 L TENSOR REMARK 3 L11: -0.0061 L22: 0.2875 REMARK 3 L33: 1.8416 L12: -0.3149 REMARK 3 L13: -0.7873 L23: 0.9800 REMARK 3 S TENSOR REMARK 3 S11: 0.1660 S12: -0.0262 S13: 0.0729 REMARK 3 S21: -0.1845 S22: 0.0145 S23: -0.0811 REMARK 3 S31: -0.6144 S32: -0.0566 S33: 0.0153 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 8G0P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1000271067. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97910 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36742 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 40.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 4.03000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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 (%): 51.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) POLYETHYLENE GLYCOL 4000, REMARK 280 0.1 M TRIS PH 8.6, AND 0.2 M MAGNESIUM CHLORIDE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 24.95150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.12950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 24.95150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.12950 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP B 55 O HOH B 101 2.05 REMARK 500 O GLU A 31 O HOH A 201 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 OE1 GLU A 23 NZ LYS A 33 2555 2.14 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 ASN A 3 -51.97 -128.30 REMARK 500 GLU A 5 -70.56 -57.98 REMARK 500 PRO A 59 -166.03 -78.46 REMARK 500 GLU A 77 97.84 54.08 REMARK 500 ASN A 81 74.40 65.69 REMARK 500 REMARK 500 REMARK: NULL DBREF 8G0P A 3 142 UNP O14777 NDC80_HUMAN 370 509 DBREF 8G0P B 2 97 UNP Q9BZD4 NUF2_HUMAN 252 347 SEQADV 8G0P SER A 1 UNP O14777 EXPRESSION TAG SEQADV 8G0P CYS A 2 UNP O14777 EXPRESSION TAG SEQADV 8G0P CYS A 143 UNP O14777 CLONING ARTIFACT SEQADV 8G0P CYS B 1 UNP Q9BZD4 EXPRESSION TAG SEQADV 8G0P CYS B 98 UNP Q9BZD4 CLONING ARTIFACT SEQRES 1 A 143 SER CYS ASN HIS GLU ARG ASN GLU LEU GLN GLN THR ILE SEQRES 2 A 143 ASN LYS LEU THR LYS ASP LEU GLU ALA GLU GLN GLN LYS SEQRES 3 A 143 LEU TRP ASN GLU GLU LEU LYS TYR ALA ARG GLY LYS GLU SEQRES 4 A 143 ALA ILE GLU THR GLN LEU ALA GLU TYR HIS LYS LEU ALA SEQRES 5 A 143 ARG LYS LEU LYS LEU ILE PRO LYS GLY ALA GLU ASN SER SEQRES 6 A 143 LYS GLY TYR ASP PHE GLU ILE LYS PHE ASN PRO GLU ALA SEQRES 7 A 143 GLY ALA ASN CYS LEU VAL LYS TYR ARG ALA GLN VAL TYR SEQRES 8 A 143 VAL PRO LEU LYS GLU LEU LEU ASN GLU THR GLU GLU GLU SEQRES 9 A 143 ILE ASN LYS ALA LEU ASN LYS LYS MET GLY LEU GLU ASP SEQRES 10 A 143 THR LEU GLU GLN LEU ASN ALA MET ILE THR GLU SER LYS SEQRES 11 A 143 ARG SER VAL ARG THR LEU LYS GLU GLU VAL GLN LYS CYS SEQRES 1 B 98 CYS LYS ASN TYR LYS GLU LYS MET LYS ASP THR VAL GLN SEQRES 2 B 98 LYS LEU LYS ASN ALA ARG GLN GLU VAL VAL GLU LYS TYR SEQRES 3 B 98 GLU ILE TYR GLY ASP SER VAL ASP CYS LEU PRO SER CYS SEQRES 4 B 98 GLN LEU GLU VAL GLN LEU TYR GLN LYS LYS ILE GLN ASP SEQRES 5 B 98 LEU SER ASP ASN ARG GLU LYS LEU ALA SER ILE LEU LYS SEQRES 6 B 98 GLU SER LEU ASN LEU GLU ASP GLN ILE GLU SER ASP GLU SEQRES 7 B 98 SER GLU LEU LYS LYS LEU LYS THR GLU GLU ASN SER PHE SEQRES 8 B 98 LYS ARG LEU MET ILE VAL CYS FORMUL 3 HOH *13(H2 O) HELIX 1 AA1 ASN A 3 LEU A 55 1 53 HELIX 2 AA2 LEU A 83 LYS A 85 5 3 HELIX 3 AA3 TYR A 86 CYS A 143 1 58 HELIX 4 AA4 LYS B 2 VAL B 97 1 96 SSBOND 1 CYS A 2 CYS A 2 1555 2554 2.03 CISPEP 1 ILE A 58 PRO A 59 0 3.26 CRYST1 49.903 72.259 80.065 90.00 98.56 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 0.020039 0.000000 0.003016 0.00000 SCALE2 0.000000 0.013839 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012631 0.00000