HEADER MOTOR PROTEIN 25-AUG-21 7RYQ TITLE CRYO-EM MAP OF KIFBP COMPND MOL_ID: 1; COMPND 2 MOLECULE: KIF-BINDING PROTEIN; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: KIF1-BINDING PROTEIN,KINESIN FAMILY BINDING PROTEIN; COMPND 5 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: KIFBP, KBP, KIAA1279, KIF1BP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINESIN REGULATION PROTEIN, MOTOR PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Z.TAN,A.L.SOLON,M.A.CIANFROCCO REVDAT 2 01-DEC-21 7RYQ 1 JRNL REVDAT 1 08-SEP-21 7RYQ 0 JRNL AUTH A.L.SOLON,Z.TAN,K.L.SCHUTT,L.JEPSEN,S.E.HAYNES, JRNL AUTH 2 A.I.NESVIZHSKII,D.SEPT,J.STUMPFF,R.OHI,M.A.CIANFROCCO JRNL TITL KINESIN-BINDING PROTEIN REMODELS THE KINESIN MOTOR TO JRNL TITL 2 PREVENT MICROTUBULE BINDING. JRNL REF SCI ADV V. 7 J9812 2021 JRNL REFN ESSN 2375-2548 JRNL PMID 34797717 JRNL DOI 10.1126/SCIADV.ABJ9812 REMARK 2 REMARK 2 RESOLUTION. 4.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, COOT, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.600 REMARK 3 NUMBER OF PARTICLES : 154176 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7RYQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1000259256. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : KIFBP MOLECULE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 4.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.70 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS GLACIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6500.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: 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 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 MET B 1 REMARK 465 ALA B 2 REMARK 465 ASN B 3 REMARK 465 VAL B 4 REMARK 465 GLU B 23 REMARK 465 LEU B 24 REMARK 465 HIS B 25 REMARK 465 LYS B 26 REMARK 465 ASN B 27 REMARK 465 PRO B 28 REMARK 465 GLU B 29 REMARK 465 LYS B 30 REMARK 465 GLU B 31 REMARK 465 GLU B 55 REMARK 465 ASP B 56 REMARK 465 GLU B 57 REMARK 465 ASP B 58 REMARK 465 GLU B 59 REMARK 465 ARG B 60 REMARK 465 PRO B 61 REMARK 465 GLU B 62 REMARK 465 ALA B 63 REMARK 465 GLU B 64 REMARK 465 ASP B 65 REMARK 465 GLY B 66 REMARK 465 PRO B 67 REMARK 465 GLY B 68 REMARK 465 ALA B 69 REMARK 465 GLY B 70 REMARK 465 ASP B 71 REMARK 465 HIS B 72 REMARK 465 ALA B 73 REMARK 465 LEU B 74 REMARK 465 GLY B 75 REMARK 465 LEU B 76 REMARK 465 PRO B 77 REMARK 465 ALA B 78 REMARK 465 GLU B 79 REMARK 465 VAL B 80 REMARK 465 VAL B 81 REMARK 465 GLU B 82 REMARK 465 PRO B 83 REMARK 465 GLU B 84 REMARK 465 GLY B 85 REMARK 465 ARG B 129 REMARK 465 LEU B 130 REMARK 465 SER B 131 REMARK 465 HIS B 132 REMARK 465 ASP B 133 REMARK 465 CYS B 134 REMARK 465 LYS B 174 REMARK 465 GLU B 175 REMARK 465 VAL B 176 REMARK 465 GLY B 177 REMARK 465 SER B 178 REMARK 465 PRO B 179 REMARK 465 PRO B 180 REMARK 465 LEU B 181 REMARK 465 ASP B 182 REMARK 465 PRO B 183 REMARK 465 THR B 184 REMARK 465 GLU B 185 REMARK 465 ARG B 186 REMARK 465 PHE B 187 REMARK 465 LEU B 188 REMARK 465 PRO B 189 REMARK 465 GLU B 190 REMARK 465 GLU B 191 REMARK 465 GLU B 192 REMARK 465 LYS B 193 REMARK 465 LEU B 194 REMARK 465 THR B 195 REMARK 465 GLU B 196 REMARK 465 GLN B 197 REMARK 465 GLU B 198 REMARK 465 ARG B 199 REMARK 465 THR B 283 REMARK 465 GLY B 284 REMARK 465 LYS B 285 REMARK 465 ILE B 286 REMARK 465 SER B 287 REMARK 465 ALA B 288 REMARK 465 THR B 289 REMARK 465 GLU B 290 REMARK 465 ASP B 291 REMARK 465 THR B 292 REMARK 465 PRO B 293 REMARK 465 GLU B 294 REMARK 465 ALA B 295 REMARK 465 GLU B 296 REMARK 465 GLY B 297 REMARK 465 GLU B 298 REMARK 465 VAL B 299 REMARK 465 PRO B 300 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 CA SER B 523 CG PRO B 527 1.25 REMARK 500 N SER B 523 CG PRO B 527 1.40 REMARK 500 O ASP B 522 CD PRO B 527 1.61 REMARK 500 NE ARG B 525 OE1 GLU B 533 1.72 REMARK 500 CD ARG B 525 OE1 GLU B 533 1.72 REMARK 500 C ASP B 522 CG PRO B 527 1.92 REMARK 500 ND2 ASN B 528 N PHE B 531 1.96 REMARK 500 NH2 ARG B 525 N GLU B 537 1.99 REMARK 500 C ASP B 522 CD PRO B 527 2.00 REMARK 500 O ASP B 439 NH2 ARG B 443 2.00 REMARK 500 O PHE B 365 N THR B 367 2.11 REMARK 500 O ARG B 443 ND1 HIS B 447 2.13 REMARK 500 CD ARG B 525 CD GLU B 533 2.13 REMARK 500 CA SER B 523 CB PRO B 527 2.14 REMARK 500 O MET B 618 OG1 THR B 621 2.14 REMARK 500 O ILE B 147 OG SER B 150 2.14 REMARK 500 NH2 ARG B 525 CA GLY B 536 2.17 REMARK 500 O ILE B 97 N LEU B 101 2.18 REMARK 500 O LEU B 17 OG SER B 20 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 ARG B 21 1.29 -64.49 REMARK 500 LYS B 34 -1.90 68.40 REMARK 500 SER B 38 -3.54 66.23 REMARK 500 PRO B 52 48.89 -80.10 REMARK 500 SER B 112 -32.94 -168.74 REMARK 500 LYS B 205 -29.23 -151.07 REMARK 500 GLU B 222 30.35 72.05 REMARK 500 ALA B 276 6.85 -67.51 REMARK 500 GLN B 326 13.06 -69.20 REMARK 500 PHE B 365 -84.01 -126.77 REMARK 500 SER B 382 -14.06 -49.87 REMARK 500 ASP B 413 -4.05 63.01 REMARK 500 ASP B 439 137.35 -171.82 REMARK 500 PRO B 463 65.34 -68.94 REMARK 500 PRO B 498 -166.60 -75.39 REMARK 500 ARG B 525 -88.60 -79.26 REMARK 500 GLU B 588 -1.17 65.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-24745 RELATED DB: EMDB REMARK 900 CRYO-EM MAP OF KIFBP DBREF 7RYQ B 1 621 UNP Q96EK5 KBP_HUMAN 1 621 SEQRES 1 B 621 MET ALA ASN VAL PRO TRP ALA GLU VAL CYS GLU LYS PHE SEQRES 2 B 621 GLN ALA ALA LEU ALA LEU SER ARG VAL GLU LEU HIS LYS SEQRES 3 B 621 ASN PRO GLU LYS GLU PRO TYR LYS SER LYS TYR SER ALA SEQRES 4 B 621 ARG ALA LEU LEU GLU GLU VAL LYS ALA LEU LEU GLY PRO SEQRES 5 B 621 ALA PRO GLU ASP GLU ASP GLU ARG PRO GLU ALA GLU ASP SEQRES 6 B 621 GLY PRO GLY ALA GLY ASP HIS ALA LEU GLY LEU PRO ALA SEQRES 7 B 621 GLU VAL VAL GLU PRO GLU GLY PRO VAL ALA GLN ARG ALA SEQRES 8 B 621 VAL ARG LEU ALA VAL ILE GLU PHE HIS LEU GLY VAL ASN SEQRES 9 B 621 HIS ILE ASP THR GLU GLU LEU SER ALA GLY GLU GLU HIS SEQRES 10 B 621 LEU VAL LYS CYS LEU ARG LEU LEU ARG ARG TYR ARG LEU SEQRES 11 B 621 SER HIS ASP CYS ILE SER LEU CYS ILE GLN ALA GLN ASN SEQRES 12 B 621 ASN LEU GLY ILE LEU TRP SER GLU ARG GLU GLU ILE GLU SEQRES 13 B 621 THR ALA GLN ALA TYR LEU GLU SER SER GLU ALA LEU TYR SEQRES 14 B 621 ASN GLN TYR MET LYS GLU VAL GLY SER PRO PRO LEU ASP SEQRES 15 B 621 PRO THR GLU ARG PHE LEU PRO GLU GLU GLU LYS LEU THR SEQRES 16 B 621 GLU GLN GLU ARG SER LYS ARG PHE GLU LYS VAL TYR THR SEQRES 17 B 621 HIS ASN LEU TYR TYR LEU ALA GLN VAL TYR GLN HIS LEU SEQRES 18 B 621 GLU MET PHE GLU LYS ALA ALA HIS TYR CYS HIS SER THR SEQRES 19 B 621 LEU LYS ARG GLN LEU GLU HIS ASN ALA TYR HIS PRO ILE SEQRES 20 B 621 GLU TRP ALA ILE ASN ALA ALA THR LEU SER GLN PHE TYR SEQRES 21 B 621 ILE ASN LYS LEU CYS PHE MET GLU ALA ARG HIS CYS LEU SEQRES 22 B 621 SER ALA ALA ASN VAL ILE PHE GLY GLN THR GLY LYS ILE SEQRES 23 B 621 SER ALA THR GLU ASP THR PRO GLU ALA GLU GLY GLU VAL SEQRES 24 B 621 PRO GLU LEU TYR HIS GLN ARG LYS GLY GLU ILE ALA ARG SEQRES 25 B 621 CYS TRP ILE LYS TYR CYS LEU THR LEU MET GLN ASN ALA SEQRES 26 B 621 GLN LEU SER MET GLN ASP ASN ILE GLY GLU LEU ASP LEU SEQRES 27 B 621 ASP LYS GLN SER GLU LEU ARG ALA LEU ARG LYS LYS GLU SEQRES 28 B 621 LEU ASP GLU GLU GLU SER ILE ARG LYS LYS ALA VAL GLN SEQRES 29 B 621 PHE GLY THR GLY GLU LEU CYS ASP ALA ILE SER ALA VAL SEQRES 30 B 621 GLU GLU LYS VAL SER TYR LEU ARG PRO LEU ASP PHE GLU SEQRES 31 B 621 GLU ALA ARG GLU LEU PHE LEU LEU GLY GLN HIS TYR VAL SEQRES 32 B 621 PHE GLU ALA LYS GLU PHE PHE GLN ILE ASP GLY TYR VAL SEQRES 33 B 621 THR ASP HIS ILE GLU VAL VAL GLN ASP HIS SER ALA LEU SEQRES 34 B 621 PHE LYS VAL LEU ALA PHE PHE GLU THR ASP MET GLU ARG SEQRES 35 B 621 ARG CYS LYS MET HIS LYS ARG ARG ILE ALA MET LEU GLU SEQRES 36 B 621 PRO LEU THR VAL ASP LEU ASN PRO GLN TYR TYR LEU LEU SEQRES 37 B 621 VAL ASN ARG GLN ILE GLN PHE GLU ILE ALA HIS ALA TYR SEQRES 38 B 621 TYR ASP MET MET ASP LEU LYS VAL ALA ILE ALA ASP ARG SEQRES 39 B 621 LEU ARG ASP PRO ASP SER HIS ILE VAL LYS LYS ILE ASN SEQRES 40 B 621 ASN LEU ASN LYS SER ALA LEU LYS TYR TYR GLN LEU PHE SEQRES 41 B 621 LEU ASP SER LEU ARG ASP PRO ASN LYS VAL PHE PRO GLU SEQRES 42 B 621 HIS ILE GLY GLU ASP VAL LEU ARG PRO ALA MET LEU ALA SEQRES 43 B 621 LYS PHE ARG VAL ALA ARG LEU TYR GLY LYS ILE ILE THR SEQRES 44 B 621 ALA ASP PRO LYS LYS GLU LEU GLU ASN LEU ALA THR SER SEQRES 45 B 621 LEU GLU HIS TYR LYS PHE ILE VAL ASP TYR CYS GLU LYS SEQRES 46 B 621 HIS PRO GLU ALA ALA GLN GLU ILE GLU VAL GLU LEU GLU SEQRES 47 B 621 LEU SER LYS GLU MET VAL SER LEU LEU PRO THR LYS MET SEQRES 48 B 621 GLU ARG PHE ARG THR LYS MET ALA LEU THR HELIX 1 AA1 PRO B 5 ARG B 21 1 17 HELIX 2 AA2 SER B 38 GLY B 51 1 14 HELIX 3 AA3 VAL B 87 ALA B 95 1 9 HELIX 4 AA4 ALA B 95 HIS B 105 1 11 HELIX 5 AA5 SER B 112 TYR B 128 1 17 HELIX 6 AA6 SER B 136 ARG B 152 1 17 HELIX 7 AA7 GLU B 154 MET B 173 1 20 HELIX 8 AA8 LYS B 201 VAL B 206 1 6 HELIX 9 AA9 VAL B 206 GLN B 219 1 14 HELIX 10 AB1 MET B 223 LEU B 239 1 17 HELIX 11 AB2 HIS B 245 LEU B 264 1 20 HELIX 12 AB3 CYS B 265 PHE B 280 1 16 HELIX 13 AB4 LEU B 302 ARG B 306 1 5 HELIX 14 AB5 ARG B 306 ALA B 325 1 20 HELIX 15 AB6 GLN B 326 SER B 328 5 3 HELIX 16 AB7 ALA B 346 GLN B 364 1 19 HELIX 17 AB8 GLY B 368 VAL B 381 1 14 HELIX 18 AB9 PHE B 389 PHE B 410 1 22 HELIX 19 AC1 TYR B 415 ALA B 434 1 20 HELIX 20 AC2 MET B 440 ASP B 460 1 21 HELIX 21 AC3 GLN B 464 ALA B 492 1 29 HELIX 22 AC4 SER B 500 ARG B 525 1 26 HELIX 23 AC5 VAL B 539 GLY B 555 1 17 HELIX 24 AC6 ALA B 560 GLU B 584 1 25 HELIX 25 AC7 GLN B 591 THR B 621 1 31 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000