HEADER PROTEIN FIBRIL 22-APR-24 8Z93 TITLE CRYO-EM STRUCTURE OF AMYLOID FIBRIL FORMED BY HUMAN RIPK1 RHIM PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 1; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: CELL DEATH PROTEIN RIP,RECEPTOR-INTERACTING PROTEIN 1,RIP-1; COMPND 5 EC: 2.7.11.1; COMPND 6 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: RIPK1, RIP, RIP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AMYOLID FIBRIL, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR Y.MA,K.ZHAO,C.LIU REVDAT 2 16-JUL-25 8Z93 1 REMARK REVDAT 1 30-APR-25 8Z93 0 JRNL AUTH Y.MA,K.ZHAO,C.LIU JRNL TITL CRYO-EM STRUCTURE OF AMYLOID FIBRIL FORMED BY HUMAN RIPK1 JRNL TITL 2 RHIM PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 4.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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 : 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) : 4.650 REMARK 3 NUMBER OF PARTICLES : 67812 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 8Z93 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 29-APR-24. REMARK 100 THE DEPOSITION ID IS D_1300047229. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : HELICAL ARRAY REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : HUMAN RIPK1 RHIM AMYOID FIBRIL 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 : 4.00 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1300.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2300.00 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) : 5500.00 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 A 494 REMARK 465 GLY A 495 REMARK 465 HIS A 496 REMARK 465 MET A 497 REMARK 465 PRO A 498 REMARK 465 SER A 499 REMARK 465 LEU A 500 REMARK 465 HIS A 501 REMARK 465 ASN A 502 REMARK 465 ILE A 503 REMARK 465 PRO A 504 REMARK 465 VAL A 505 REMARK 465 PRO A 506 REMARK 465 GLU A 507 REMARK 465 THR A 508 REMARK 465 ASN A 509 REMARK 465 TYR A 510 REMARK 465 LEU A 511 REMARK 465 GLY A 512 REMARK 465 ASN A 513 REMARK 465 THR A 514 REMARK 465 PRO A 515 REMARK 465 THR A 516 REMARK 465 MET A 517 REMARK 465 PRO A 518 REMARK 465 PHE A 519 REMARK 465 SER A 520 REMARK 465 SER A 521 REMARK 465 LEU A 522 REMARK 465 PRO A 523 REMARK 465 PRO A 524 REMARK 465 THR A 525 REMARK 465 ASP A 526 REMARK 465 GLU A 527 REMARK 465 SER A 528 REMARK 465 ILE A 529 REMARK 465 LYS A 530 REMARK 465 GLY A 551 REMARK 465 THR A 552 REMARK 465 SER A 553 REMARK 465 SER A 554 REMARK 465 SER A 555 REMARK 465 LEU A 556 REMARK 465 LEU A 557 REMARK 465 ASP A 558 REMARK 465 SER A 559 REMARK 465 THR A 560 REMARK 465 ASN A 561 REMARK 465 THR A 562 REMARK 465 ASN A 563 REMARK 465 PHE A 564 REMARK 465 LYS A 565 REMARK 465 GLU A 566 REMARK 465 GLU A 567 REMARK 465 PRO A 568 REMARK 465 ALA A 569 REMARK 465 ALA A 570 REMARK 465 LYS A 571 REMARK 465 TYR A 572 REMARK 465 GLN A 573 REMARK 465 ALA A 574 REMARK 465 ILE A 575 REMARK 465 PHE A 576 REMARK 465 ASP A 577 REMARK 465 ASN A 578 REMARK 465 THR A 579 REMARK 465 THR A 580 REMARK 465 SER A 581 REMARK 465 LEU A 582 REMARK 465 THR A 583 REMARK 465 LEU A 584 REMARK 465 GLU A 585 REMARK 465 HIS A 586 REMARK 465 HIS A 587 REMARK 465 HIS A 588 REMARK 465 HIS A 589 REMARK 465 HIS A 590 REMARK 465 HIS A 591 REMARK 465 MET B 494 REMARK 465 GLY B 495 REMARK 465 HIS B 496 REMARK 465 MET B 497 REMARK 465 PRO B 498 REMARK 465 SER B 499 REMARK 465 LEU B 500 REMARK 465 HIS B 501 REMARK 465 ASN B 502 REMARK 465 ILE B 503 REMARK 465 PRO B 504 REMARK 465 VAL B 505 REMARK 465 PRO B 506 REMARK 465 GLU B 507 REMARK 465 THR B 508 REMARK 465 ASN B 509 REMARK 465 TYR B 510 REMARK 465 LEU B 511 REMARK 465 GLY B 512 REMARK 465 ASN B 513 REMARK 465 THR B 514 REMARK 465 PRO B 515 REMARK 465 THR B 516 REMARK 465 MET B 517 REMARK 465 PRO B 518 REMARK 465 PHE B 519 REMARK 465 SER B 520 REMARK 465 SER B 521 REMARK 465 LEU B 522 REMARK 465 PRO B 523 REMARK 465 PRO B 524 REMARK 465 THR B 525 REMARK 465 ASP B 526 REMARK 465 GLU B 527 REMARK 465 SER B 528 REMARK 465 ILE B 529 REMARK 465 LYS B 530 REMARK 465 GLY B 551 REMARK 465 THR B 552 REMARK 465 SER B 553 REMARK 465 SER B 554 REMARK 465 SER B 555 REMARK 465 LEU B 556 REMARK 465 LEU B 557 REMARK 465 ASP B 558 REMARK 465 SER B 559 REMARK 465 THR B 560 REMARK 465 ASN B 561 REMARK 465 THR B 562 REMARK 465 ASN B 563 REMARK 465 PHE B 564 REMARK 465 LYS B 565 REMARK 465 GLU B 566 REMARK 465 GLU B 567 REMARK 465 PRO B 568 REMARK 465 ALA B 569 REMARK 465 ALA B 570 REMARK 465 LYS B 571 REMARK 465 TYR B 572 REMARK 465 GLN B 573 REMARK 465 ALA B 574 REMARK 465 ILE B 575 REMARK 465 PHE B 576 REMARK 465 ASP B 577 REMARK 465 ASN B 578 REMARK 465 THR B 579 REMARK 465 THR B 580 REMARK 465 SER B 581 REMARK 465 LEU B 582 REMARK 465 THR B 583 REMARK 465 LEU B 584 REMARK 465 GLU B 585 REMARK 465 HIS B 586 REMARK 465 HIS B 587 REMARK 465 HIS B 588 REMARK 465 HIS B 589 REMARK 465 HIS B 590 REMARK 465 HIS B 591 REMARK 465 MET C 494 REMARK 465 GLY C 495 REMARK 465 HIS C 496 REMARK 465 MET C 497 REMARK 465 PRO C 498 REMARK 465 SER C 499 REMARK 465 LEU C 500 REMARK 465 HIS C 501 REMARK 465 ASN C 502 REMARK 465 ILE C 503 REMARK 465 PRO C 504 REMARK 465 VAL C 505 REMARK 465 PRO C 506 REMARK 465 GLU C 507 REMARK 465 THR C 508 REMARK 465 ASN C 509 REMARK 465 TYR C 510 REMARK 465 LEU C 511 REMARK 465 GLY C 512 REMARK 465 ASN C 513 REMARK 465 THR C 514 REMARK 465 PRO C 515 REMARK 465 THR C 516 REMARK 465 MET C 517 REMARK 465 PRO C 518 REMARK 465 PHE C 519 REMARK 465 SER C 520 REMARK 465 SER C 521 REMARK 465 LEU C 522 REMARK 465 PRO C 523 REMARK 465 PRO C 524 REMARK 465 THR C 525 REMARK 465 ASP C 526 REMARK 465 GLU C 527 REMARK 465 SER C 528 REMARK 465 ILE C 529 REMARK 465 LYS C 530 REMARK 465 GLY C 551 REMARK 465 THR C 552 REMARK 465 SER C 553 REMARK 465 SER C 554 REMARK 465 SER C 555 REMARK 465 LEU C 556 REMARK 465 LEU C 557 REMARK 465 ASP C 558 REMARK 465 SER C 559 REMARK 465 THR C 560 REMARK 465 ASN C 561 REMARK 465 THR C 562 REMARK 465 ASN C 563 REMARK 465 PHE C 564 REMARK 465 LYS C 565 REMARK 465 GLU C 566 REMARK 465 GLU C 567 REMARK 465 PRO C 568 REMARK 465 ALA C 569 REMARK 465 ALA C 570 REMARK 465 LYS C 571 REMARK 465 TYR C 572 REMARK 465 GLN C 573 REMARK 465 ALA C 574 REMARK 465 ILE C 575 REMARK 465 PHE C 576 REMARK 465 ASP C 577 REMARK 465 ASN C 578 REMARK 465 THR C 579 REMARK 465 THR C 580 REMARK 465 SER C 581 REMARK 465 LEU C 582 REMARK 465 THR C 583 REMARK 465 LEU C 584 REMARK 465 GLU C 585 REMARK 465 HIS C 586 REMARK 465 HIS C 587 REMARK 465 HIS C 588 REMARK 465 HIS C 589 REMARK 465 HIS C 590 REMARK 465 HIS C 591 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 N TYR B 531 OG1 THR C 532 2.06 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 ILE A 533 -67.22 -98.98 REMARK 500 TYR A 534 55.21 35.68 REMARK 500 ASN A 535 -162.35 -78.47 REMARK 500 ALA A 543 -168.07 -160.96 REMARK 500 TYR A 546 -179.65 -68.12 REMARK 500 ILE B 533 -67.27 -98.92 REMARK 500 TYR B 534 55.20 35.69 REMARK 500 ASN B 535 -162.26 -78.48 REMARK 500 ALA B 543 -168.01 -160.99 REMARK 500 TYR B 546 -179.61 -68.14 REMARK 500 ILE C 533 -67.28 -98.95 REMARK 500 TYR C 534 55.20 35.71 REMARK 500 ASN C 535 -162.35 -78.41 REMARK 500 ALA C 543 -168.03 -160.97 REMARK 500 TYR C 546 -179.62 -68.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-39853 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF AMYLOID FIBRIL FORMED BY HUMAN RIPK1 RHIM REMARK 900 PROTEIN DBREF 8Z93 A 496 583 UNP Q13546 RIPK1_HUMAN 496 583 DBREF 8Z93 B 496 583 UNP Q13546 RIPK1_HUMAN 496 583 DBREF 8Z93 C 496 583 UNP Q13546 RIPK1_HUMAN 496 583 SEQADV 8Z93 MET A 494 UNP Q13546 INITIATING METHIONINE SEQADV 8Z93 GLY A 495 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 LEU A 584 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 GLU A 585 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS A 586 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS A 587 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS A 588 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS A 589 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS A 590 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS A 591 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 MET B 494 UNP Q13546 INITIATING METHIONINE SEQADV 8Z93 GLY B 495 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 LEU B 584 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 GLU B 585 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS B 586 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS B 587 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS B 588 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS B 589 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS B 590 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS B 591 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 MET C 494 UNP Q13546 INITIATING METHIONINE SEQADV 8Z93 GLY C 495 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 LEU C 584 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 GLU C 585 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS C 586 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS C 587 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS C 588 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS C 589 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS C 590 UNP Q13546 EXPRESSION TAG SEQADV 8Z93 HIS C 591 UNP Q13546 EXPRESSION TAG SEQRES 1 A 98 MET GLY HIS MET PRO SER LEU HIS ASN ILE PRO VAL PRO SEQRES 2 A 98 GLU THR ASN TYR LEU GLY ASN THR PRO THR MET PRO PHE SEQRES 3 A 98 SER SER LEU PRO PRO THR ASP GLU SER ILE LYS TYR THR SEQRES 4 A 98 ILE TYR ASN SER THR GLY ILE GLN ILE GLY ALA TYR ASN SEQRES 5 A 98 TYR MET GLU ILE GLY GLY THR SER SER SER LEU LEU ASP SEQRES 6 A 98 SER THR ASN THR ASN PHE LYS GLU GLU PRO ALA ALA LYS SEQRES 7 A 98 TYR GLN ALA ILE PHE ASP ASN THR THR SER LEU THR LEU SEQRES 8 A 98 GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 98 MET GLY HIS MET PRO SER LEU HIS ASN ILE PRO VAL PRO SEQRES 2 B 98 GLU THR ASN TYR LEU GLY ASN THR PRO THR MET PRO PHE SEQRES 3 B 98 SER SER LEU PRO PRO THR ASP GLU SER ILE LYS TYR THR SEQRES 4 B 98 ILE TYR ASN SER THR GLY ILE GLN ILE GLY ALA TYR ASN SEQRES 5 B 98 TYR MET GLU ILE GLY GLY THR SER SER SER LEU LEU ASP SEQRES 6 B 98 SER THR ASN THR ASN PHE LYS GLU GLU PRO ALA ALA LYS SEQRES 7 B 98 TYR GLN ALA ILE PHE ASP ASN THR THR SER LEU THR LEU SEQRES 8 B 98 GLU HIS HIS HIS HIS HIS HIS SEQRES 1 C 98 MET GLY HIS MET PRO SER LEU HIS ASN ILE PRO VAL PRO SEQRES 2 C 98 GLU THR ASN TYR LEU GLY ASN THR PRO THR MET PRO PHE SEQRES 3 C 98 SER SER LEU PRO PRO THR ASP GLU SER ILE LYS TYR THR SEQRES 4 C 98 ILE TYR ASN SER THR GLY ILE GLN ILE GLY ALA TYR ASN SEQRES 5 C 98 TYR MET GLU ILE GLY GLY THR SER SER SER LEU LEU ASP SEQRES 6 C 98 SER THR ASN THR ASN PHE LYS GLU GLU PRO ALA ALA LYS SEQRES 7 C 98 TYR GLN ALA ILE PHE ASP ASN THR THR SER LEU THR LEU SEQRES 8 C 98 GLU HIS HIS HIS HIS HIS HIS 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 TER 160 GLY A 550 TER 320 GLY B 550 TER 480 GLY C 550 MASTER 381 0 0 0 0 0 0 6 477 3 0 24 END