HEADER TRANSPORT PROTEIN 07-FEB-25 9N87 TITLE CRYO-EM STRUCTURE OF HUMAN IMPORTIN BETA: XIBB COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMPORTIN SUBUNIT BETA-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IMPORTIN-90,KARYOPHERIN SUBUNIT BETA-1,NUCLEAR FACTOR P97, COMPND 5 PORE TARGETING COMPLEX 97 KDA SUBUNIT,PTAC97; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: XRIP1A; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: RESIDUES 6-47; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: MODELED SEQUENCE IS FROM HOMO SAPIENS (UNP Q86UA6) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KPNB1, NTF97; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 10 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 11 ORGANISM_TAXID: 8355; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IMPORTINS, TRANSPORT PROTEIN, RAN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.KO,J.LI,G.CINGOLANI REVDAT 1 10-DEC-25 9N87 0 JRNL AUTH Y.KO,G.CINGOLANI JRNL TITL CRYO-EM STRUCTURE OF HUMAN IMPORTIN BETA-RAN-GTP HETERODIMER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL 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) : 3.400 REMARK 3 NUMBER OF PARTICLES : 293677 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9N87 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1000292057. 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 : IMPORTIN BETA/RANGTP REMARK 245 HETERODIMER REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 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 KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 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: DIMERIC 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: 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 VAL A 43 -54.45 -126.54 REMARK 500 ARG A 88 -17.79 69.92 REMARK 500 GLU A 102 -133.00 63.10 REMARK 500 SER A 108 -2.18 69.58 REMARK 500 LYS A 243 -10.39 72.01 REMARK 500 GLU A 360 -124.79 56.14 REMARK 500 TRP A 472 -8.78 76.06 REMARK 500 SER A 476 -2.16 65.58 REMARK 500 GLU A 493 149.82 -171.45 REMARK 500 PRO A 517 0.43 -69.52 REMARK 500 ASN A 538 34.09 -99.20 REMARK 500 SER A 617 -119.53 44.53 REMARK 500 SER A 621 135.19 -172.56 REMARK 500 GLN A 682 -136.95 56.03 REMARK 500 GLU A 703 58.38 -94.92 REMARK 500 PRO A 841 0.84 -64.88 REMARK 500 ALA B 2 -99.05 56.05 REMARK 500 GLU B 3 -147.46 55.22 REMARK 500 SER B 4 -161.68 54.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-49117 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN IMPORTIN BETA: XIBB COMPLEX REMARK 999 REMARK 999 SEQUENCE REMARK 999 MODELED SEQUENCE FOR XRIP1A IS FROM HOMO SAPIENS (UNP Q86UA6). DBREF 9N87 A 1 876 UNP Q14974 IMB1_HUMAN 1 876 DBREF 9N87 B 1 45 PDB 9N87 9N87 1 45 SEQRES 1 A 876 MET GLU LEU ILE THR ILE LEU GLU LYS THR VAL SER PRO SEQRES 2 A 876 ASP ARG LEU GLU LEU GLU ALA ALA GLN LYS PHE LEU GLU SEQRES 3 A 876 ARG ALA ALA VAL GLU ASN LEU PRO THR PHE LEU VAL GLU SEQRES 4 A 876 LEU SER ARG VAL LEU ALA ASN PRO GLY ASN SER GLN VAL SEQRES 5 A 876 ALA ARG VAL ALA ALA GLY LEU GLN ILE LYS ASN SER LEU SEQRES 6 A 876 THR SER LYS ASP PRO ASP ILE LYS ALA GLN TYR GLN GLN SEQRES 7 A 876 ARG TRP LEU ALA ILE ASP ALA ASN ALA ARG ARG GLU VAL SEQRES 8 A 876 LYS ASN TYR VAL LEU GLN THR LEU GLY THR GLU THR TYR SEQRES 9 A 876 ARG PRO SER SER ALA SER GLN CYS VAL ALA GLY ILE ALA SEQRES 10 A 876 CYS ALA GLU ILE PRO VAL ASN GLN TRP PRO GLU LEU ILE SEQRES 11 A 876 PRO GLN LEU VAL ALA ASN VAL THR ASN PRO ASN SER THR SEQRES 12 A 876 GLU HIS MET LYS GLU SER THR LEU GLU ALA ILE GLY TYR SEQRES 13 A 876 ILE CYS GLN ASP ILE ASP PRO GLU GLN LEU GLN ASP LYS SEQRES 14 A 876 SER ASN GLU ILE LEU THR ALA ILE ILE GLN GLY MET ARG SEQRES 15 A 876 LYS GLU GLU PRO SER ASN ASN VAL LYS LEU ALA ALA THR SEQRES 16 A 876 ASN ALA LEU LEU ASN SER LEU GLU PHE THR LYS ALA ASN SEQRES 17 A 876 PHE ASP LYS GLU SER GLU ARG HIS PHE ILE MET GLN VAL SEQRES 18 A 876 VAL CYS GLU ALA THR GLN CYS PRO ASP THR ARG VAL ARG SEQRES 19 A 876 VAL ALA ALA LEU GLN ASN LEU VAL LYS ILE MET SER LEU SEQRES 20 A 876 TYR TYR GLN TYR MET GLU THR TYR MET GLY PRO ALA LEU SEQRES 21 A 876 PHE ALA ILE THR ILE GLU ALA MET LYS SER ASP ILE ASP SEQRES 22 A 876 GLU VAL ALA LEU GLN GLY ILE GLU PHE TRP SER ASN VAL SEQRES 23 A 876 CYS ASP GLU GLU MET ASP LEU ALA ILE GLU ALA SER GLU SEQRES 24 A 876 ALA ALA GLU GLN GLY ARG PRO PRO GLU HIS THR SER LYS SEQRES 25 A 876 PHE TYR ALA LYS GLY ALA LEU GLN TYR LEU VAL PRO ILE SEQRES 26 A 876 LEU THR GLN THR LEU THR LYS GLN ASP GLU ASN ASP ASP SEQRES 27 A 876 ASP ASP ASP TRP ASN PRO CYS LYS ALA ALA GLY VAL CYS SEQRES 28 A 876 LEU MET LEU LEU ALA THR CYS CYS GLU ASP ASP ILE VAL SEQRES 29 A 876 PRO HIS VAL LEU PRO PHE ILE LYS GLU HIS ILE LYS ASN SEQRES 30 A 876 PRO ASP TRP ARG TYR ARG ASP ALA ALA VAL MET ALA PHE SEQRES 31 A 876 GLY CYS ILE LEU GLU GLY PRO GLU PRO SER GLN LEU LYS SEQRES 32 A 876 PRO LEU VAL ILE GLN ALA MET PRO THR LEU ILE GLU LEU SEQRES 33 A 876 MET LYS ASP PRO SER VAL VAL VAL ARG ASP THR ALA ALA SEQRES 34 A 876 TRP THR VAL GLY ARG ILE CYS GLU LEU LEU PRO GLU ALA SEQRES 35 A 876 ALA ILE ASN ASP VAL TYR LEU ALA PRO LEU LEU GLN CYS SEQRES 36 A 876 LEU ILE GLU GLY LEU SER ALA GLU PRO ARG VAL ALA SER SEQRES 37 A 876 ASN VAL CYS TRP ALA PHE SER SER LEU ALA GLU ALA ALA SEQRES 38 A 876 TYR GLU ALA ALA ASP VAL ALA ASP ASP GLN GLU GLU PRO SEQRES 39 A 876 ALA THR TYR CYS LEU SER SER SER PHE GLU LEU ILE VAL SEQRES 40 A 876 GLN LYS LEU LEU GLU THR THR ASP ARG PRO ASP GLY HIS SEQRES 41 A 876 GLN ASN ASN LEU ARG SER SER ALA TYR GLU SER LEU MET SEQRES 42 A 876 GLU ILE VAL LYS ASN SER ALA LYS ASP CYS TYR PRO ALA SEQRES 43 A 876 VAL GLN LYS THR THR LEU VAL ILE MET GLU ARG LEU GLN SEQRES 44 A 876 GLN VAL LEU GLN MET GLU SER HIS ILE GLN SER THR SER SEQRES 45 A 876 ASP ARG ILE GLN PHE ASN ASP LEU GLN SER LEU LEU CYS SEQRES 46 A 876 ALA THR LEU GLN ASN VAL LEU ARG LYS VAL GLN HIS GLN SEQRES 47 A 876 ASP ALA LEU GLN ILE SER ASP VAL VAL MET ALA SER LEU SEQRES 48 A 876 LEU ARG MET PHE GLN SER THR ALA GLY SER GLY GLY VAL SEQRES 49 A 876 GLN GLU ASP ALA LEU MET ALA VAL SER THR LEU VAL GLU SEQRES 50 A 876 VAL LEU GLY GLY GLU PHE LEU LYS TYR MET GLU ALA PHE SEQRES 51 A 876 LYS PRO PHE LEU GLY ILE GLY LEU LYS ASN TYR ALA GLU SEQRES 52 A 876 TYR GLN VAL CYS LEU ALA ALA VAL GLY LEU VAL GLY ASP SEQRES 53 A 876 LEU CYS ARG ALA LEU GLN SER ASN ILE ILE PRO PHE CYS SEQRES 54 A 876 ASP GLU VAL MET GLN LEU LEU LEU GLU ASN LEU GLY ASN SEQRES 55 A 876 GLU ASN VAL HIS ARG SER VAL LYS PRO GLN ILE LEU SER SEQRES 56 A 876 VAL PHE GLY ASP ILE ALA LEU ALA ILE GLY GLY GLU PHE SEQRES 57 A 876 LYS LYS TYR LEU GLU VAL VAL LEU ASN THR LEU GLN GLN SEQRES 58 A 876 ALA SER GLN ALA GLN VAL ASP LYS SER ASP TYR ASP MET SEQRES 59 A 876 VAL ASP TYR LEU ASN GLU LEU ARG GLU SER CYS LEU GLU SEQRES 60 A 876 ALA TYR THR GLY ILE VAL GLN GLY LEU LYS GLY ASP GLN SEQRES 61 A 876 GLU ASN VAL HIS PRO ASP VAL MET LEU VAL GLN PRO ARG SEQRES 62 A 876 VAL GLU PHE ILE LEU SER PHE ILE ASP HIS ILE ALA GLY SEQRES 63 A 876 ASP GLU ASP HIS THR ASP GLY VAL VAL ALA CYS ALA ALA SEQRES 64 A 876 GLY LEU ILE GLY ASP LEU CYS THR ALA PHE GLY LYS ASP SEQRES 65 A 876 VAL LEU LYS LEU VAL GLU ALA ARG PRO MET ILE HIS GLU SEQRES 66 A 876 LEU LEU THR GLU GLY ARG ARG SER LYS THR ASN LYS ALA SEQRES 67 A 876 LYS THR LEU ALA THR TRP ALA THR LYS GLU LEU ARG LYS SEQRES 68 A 876 LEU LYS ASN GLN ALA SEQRES 1 B 45 MET ALA GLU SER LEU ARG SER PRO ARG ARG SER LEU TYR SEQRES 2 B 45 LYS LEU VAL GLY SER PRO PRO TRP LYS GLU ALA PHE ARG SEQRES 3 B 45 GLN ARG CYS LEU GLU ARG MET ARG ASN SER ARG ASP ARG SEQRES 4 B 45 LEU LEU ASN ARG TYR ARG HELIX 1 AA1 GLU A 2 SER A 12 1 11 HELIX 2 AA2 ARG A 15 GLN A 22 1 8 HELIX 3 AA3 GLN A 22 ALA A 29 1 8 HELIX 4 AA4 PHE A 36 SER A 41 1 6 HELIX 5 AA5 SER A 50 THR A 66 1 17 HELIX 6 AA6 ASP A 69 ALA A 82 1 14 HELIX 7 AA7 VAL A 91 LEU A 99 1 9 HELIX 8 AA8 SER A 108 ILE A 121 1 14 HELIX 9 AA9 GLU A 128 ALA A 135 1 8 HELIX 10 AB1 ASN A 136 THR A 138 5 3 HELIX 11 AB2 THR A 143 ILE A 161 1 19 HELIX 12 AB3 GLU A 164 ASP A 168 5 5 HELIX 13 AB4 LYS A 169 ILE A 178 1 10 HELIX 14 AB5 ASN A 188 LEU A 202 1 15 HELIX 15 AB6 THR A 205 ASP A 210 1 6 HELIX 16 AB7 LYS A 211 ALA A 225 1 15 HELIX 17 AB8 ASP A 230 VAL A 242 1 13 HELIX 18 AB9 ILE A 244 TYR A 249 1 6 HELIX 19 AC1 GLN A 250 TYR A 255 5 6 HELIX 20 AC2 ALA A 259 LYS A 269 1 11 HELIX 21 AC3 ILE A 272 GLY A 304 1 33 HELIX 22 AC4 PHE A 313 ALA A 318 1 6 HELIX 23 AC5 LEU A 322 THR A 331 1 10 HELIX 24 AC6 ASN A 343 GLU A 360 1 18 HELIX 25 AC7 ASP A 362 ILE A 375 1 14 HELIX 26 AC8 ASP A 379 ILE A 393 1 15 HELIX 27 AC9 GLU A 398 MET A 417 1 20 HELIX 28 AD1 VAL A 422 LEU A 439 1 18 HELIX 29 AD2 LEU A 439 ILE A 444 1 6 HELIX 30 AD3 TYR A 448 LEU A 460 1 13 HELIX 31 AD4 GLU A 463 CYS A 471 1 9 HELIX 32 AD5 LEU A 477 ALA A 484 1 8 HELIX 33 AD6 LEU A 499 ASP A 515 1 17 HELIX 34 AD7 HIS A 520 ASN A 522 5 3 HELIX 35 AD8 ASN A 523 ASN A 538 1 16 HELIX 36 AD9 CYS A 543 VAL A 561 1 19 HELIX 37 AE1 SER A 570 ARG A 593 1 24 HELIX 38 AE2 GLN A 596 GLN A 616 1 21 HELIX 39 AE3 SER A 621 GLY A 640 1 20 HELIX 40 AE4 PHE A 643 LYS A 659 1 17 HELIX 41 AE5 GLU A 663 GLY A 675 1 13 HELIX 42 AE6 LEU A 677 GLN A 682 5 6 HELIX 43 AE7 PHE A 688 ASN A 702 1 15 HELIX 44 AE8 SER A 708 GLY A 725 1 18 HELIX 45 AE9 TYR A 731 GLN A 744 1 14 HELIX 46 AF1 ASP A 751 GLY A 778 1 28 HELIX 47 AF2 HIS A 784 PRO A 792 5 9 HELIX 48 AF3 ARG A 793 ASP A 807 1 15 HELIX 49 AF4 GLY A 813 GLY A 823 1 11 HELIX 50 AF5 ASP A 824 PHE A 829 1 6 HELIX 51 AF6 ASP A 832 VAL A 837 1 6 HELIX 52 AF7 PRO A 841 ARG A 851 1 11 HELIX 53 AF8 THR A 855 ASN A 874 1 20 HELIX 54 AF9 PRO B 20 ASN B 42 1 23 HELIX 55 AG1 ARG B 43 ARG B 45 5 3 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 MASTER 136 0 0 55 0 0 0 6 7195 2 0 72 END