HEADER PROTEIN FIBRIL 24-OCT-24 9K8S TITLE CRYO-EM STRUCTURE OF HE30 POLYMORPH 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NINJURIN-1; COMPND 3 CHAIN: E, F, G, H, I, J, K, L, M, N, O, P; COMPND 4 SYNONYM: HE30,HNINJ1,NERVE INJURY-INDUCED PROTEIN 1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS HELICAL FIBRIL, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR W.C.XIA,C.LIU REVDAT 1 29-OCT-25 9K8S 0 JRNL AUTH M.WANG,W.XIA,D.ZHAO,Z.ZHAI,R.CHEN,X.BAI,Z.ZHANG,H.FAN, JRNL AUTH 2 J.P.ZHANG,C.LIU,F.JIAO JRNL TITL AMYLOID FIBRILLATION OF A NINJURIN-1-DERIVED ALPHA-HELICAL JRNL TITL 2 PEPTIDE: STRUCTURAL INSIGHTS INTO CONFORMATIONAL TRANSITION. JRNL REF ACS NANO V. 19 35977 2025 JRNL REFN ESSN 1936-086X JRNL PMID 41037056 JRNL DOI 10.1021/ACSNANO.5C14731 REMARK 2 REMARK 2 RESOLUTION. 2.90 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) : 2.900 REMARK 3 NUMBER OF PARTICLES : 523480 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 9K8S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 01-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1300052970. 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 : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : CRYO-EM STRUCTURE OF HE30 REMARK 245 POLYMORPH 1 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 : 7.40 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) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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: DODECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, G, H, I, J, K, L, M, N, REMARK 350 AND CHAINS: O, P 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 HIS E 40 REMARK 465 TYR E 41 REMARK 465 ALA E 42 REMARK 465 VAL E 68 REMARK 465 GLU E 69 REMARK 465 HIS F 40 REMARK 465 TYR F 41 REMARK 465 ALA F 42 REMARK 465 SER F 43 REMARK 465 LYS F 44 REMARK 465 LYS F 45 REMARK 465 SER F 46 REMARK 465 ALA F 47 REMARK 465 ALA F 48 REMARK 465 GLU F 49 REMARK 465 SER F 50 REMARK 465 HIS G 40 REMARK 465 TYR G 41 REMARK 465 ALA G 42 REMARK 465 VAL G 68 REMARK 465 GLU G 69 REMARK 465 HIS H 40 REMARK 465 TYR H 41 REMARK 465 ALA H 42 REMARK 465 SER H 43 REMARK 465 LYS H 44 REMARK 465 LYS H 45 REMARK 465 SER H 46 REMARK 465 ALA H 47 REMARK 465 ALA H 48 REMARK 465 GLU H 49 REMARK 465 SER H 50 REMARK 465 HIS I 40 REMARK 465 TYR I 41 REMARK 465 ALA I 42 REMARK 465 VAL I 68 REMARK 465 GLU I 69 REMARK 465 HIS J 40 REMARK 465 TYR J 41 REMARK 465 ALA J 42 REMARK 465 SER J 43 REMARK 465 LYS J 44 REMARK 465 LYS J 45 REMARK 465 SER J 46 REMARK 465 ALA J 47 REMARK 465 ALA J 48 REMARK 465 GLU J 49 REMARK 465 SER J 50 REMARK 465 HIS K 40 REMARK 465 TYR K 41 REMARK 465 ALA K 42 REMARK 465 VAL K 68 REMARK 465 GLU K 69 REMARK 465 HIS L 40 REMARK 465 TYR L 41 REMARK 465 ALA L 42 REMARK 465 SER L 43 REMARK 465 LYS L 44 REMARK 465 LYS L 45 REMARK 465 SER L 46 REMARK 465 ALA L 47 REMARK 465 ALA L 48 REMARK 465 GLU L 49 REMARK 465 SER L 50 REMARK 465 HIS M 40 REMARK 465 TYR M 41 REMARK 465 ALA M 42 REMARK 465 VAL M 68 REMARK 465 GLU M 69 REMARK 465 HIS N 40 REMARK 465 TYR N 41 REMARK 465 ALA N 42 REMARK 465 SER N 43 REMARK 465 LYS N 44 REMARK 465 LYS N 45 REMARK 465 SER N 46 REMARK 465 ALA N 47 REMARK 465 ALA N 48 REMARK 465 GLU N 49 REMARK 465 SER N 50 REMARK 465 HIS O 40 REMARK 465 TYR O 41 REMARK 465 ALA O 42 REMARK 465 VAL O 68 REMARK 465 GLU O 69 REMARK 465 HIS P 40 REMARK 465 TYR P 41 REMARK 465 ALA P 42 REMARK 465 SER P 43 REMARK 465 LYS P 44 REMARK 465 LYS P 45 REMARK 465 SER P 46 REMARK 465 ALA P 47 REMARK 465 ALA P 48 REMARK 465 GLU P 49 REMARK 465 SER P 50 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62179 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HE30 POLYMORPH 1 DBREF 9K8S E 40 69 UNP Q92982 NINJ1_HUMAN 40 69 DBREF 9K8S F 40 69 UNP Q92982 NINJ1_HUMAN 40 69 DBREF 9K8S G 40 69 UNP Q92982 NINJ1_HUMAN 40 69 DBREF 9K8S H 40 69 UNP Q92982 NINJ1_HUMAN 40 69 DBREF 9K8S I 40 69 UNP Q92982 NINJ1_HUMAN 40 69 DBREF 9K8S J 40 69 UNP Q92982 NINJ1_HUMAN 40 69 DBREF 9K8S K 40 69 UNP Q92982 NINJ1_HUMAN 40 69 DBREF 9K8S L 40 69 UNP Q92982 NINJ1_HUMAN 40 69 DBREF 9K8S M 40 69 UNP Q92982 NINJ1_HUMAN 40 69 DBREF 9K8S N 40 69 UNP Q92982 NINJ1_HUMAN 40 69 DBREF 9K8S O 40 69 UNP Q92982 NINJ1_HUMAN 40 69 DBREF 9K8S P 40 69 UNP Q92982 NINJ1_HUMAN 40 69 SEQRES 1 E 30 HIS TYR ALA SER LYS LYS SER ALA ALA GLU SER MET LEU SEQRES 2 E 30 ASP ILE ALA LEU LEU MET ALA ASN ALA SER GLN LEU LYS SEQRES 3 E 30 ALA VAL VAL GLU SEQRES 1 F 30 HIS TYR ALA SER LYS LYS SER ALA ALA GLU SER MET LEU SEQRES 2 F 30 ASP ILE ALA LEU LEU MET ALA ASN ALA SER GLN LEU LYS SEQRES 3 F 30 ALA VAL VAL GLU SEQRES 1 G 30 HIS TYR ALA SER LYS LYS SER ALA ALA GLU SER MET LEU SEQRES 2 G 30 ASP ILE ALA LEU LEU MET ALA ASN ALA SER GLN LEU LYS SEQRES 3 G 30 ALA VAL VAL GLU SEQRES 1 H 30 HIS TYR ALA SER LYS LYS SER ALA ALA GLU SER MET LEU SEQRES 2 H 30 ASP ILE ALA LEU LEU MET ALA ASN ALA SER GLN LEU LYS SEQRES 3 H 30 ALA VAL VAL GLU SEQRES 1 I 30 HIS TYR ALA SER LYS LYS SER ALA ALA GLU SER MET LEU SEQRES 2 I 30 ASP ILE ALA LEU LEU MET ALA ASN ALA SER GLN LEU LYS SEQRES 3 I 30 ALA VAL VAL GLU SEQRES 1 J 30 HIS TYR ALA SER LYS LYS SER ALA ALA GLU SER MET LEU SEQRES 2 J 30 ASP ILE ALA LEU LEU MET ALA ASN ALA SER GLN LEU LYS SEQRES 3 J 30 ALA VAL VAL GLU SEQRES 1 K 30 HIS TYR ALA SER LYS LYS SER ALA ALA GLU SER MET LEU SEQRES 2 K 30 ASP ILE ALA LEU LEU MET ALA ASN ALA SER GLN LEU LYS SEQRES 3 K 30 ALA VAL VAL GLU SEQRES 1 L 30 HIS TYR ALA SER LYS LYS SER ALA ALA GLU SER MET LEU SEQRES 2 L 30 ASP ILE ALA LEU LEU MET ALA ASN ALA SER GLN LEU LYS SEQRES 3 L 30 ALA VAL VAL GLU SEQRES 1 M 30 HIS TYR ALA SER LYS LYS SER ALA ALA GLU SER MET LEU SEQRES 2 M 30 ASP ILE ALA LEU LEU MET ALA ASN ALA SER GLN LEU LYS SEQRES 3 M 30 ALA VAL VAL GLU SEQRES 1 N 30 HIS TYR ALA SER LYS LYS SER ALA ALA GLU SER MET LEU SEQRES 2 N 30 ASP ILE ALA LEU LEU MET ALA ASN ALA SER GLN LEU LYS SEQRES 3 N 30 ALA VAL VAL GLU SEQRES 1 O 30 HIS TYR ALA SER LYS LYS SER ALA ALA GLU SER MET LEU SEQRES 2 O 30 ASP ILE ALA LEU LEU MET ALA ASN ALA SER GLN LEU LYS SEQRES 3 O 30 ALA VAL VAL GLU SEQRES 1 P 30 HIS TYR ALA SER LYS LYS SER ALA ALA GLU SER MET LEU SEQRES 2 P 30 ASP ILE ALA LEU LEU MET ALA ASN ALA SER GLN LEU LYS SEQRES 3 P 30 ALA VAL VAL GLU SHEET 1 AA1 3 MET G 58 ALA G 59 0 SHEET 2 AA1 3 MET E 58 ALA E 59 1 N MET E 58 O ALA G 59 SHEET 3 AA1 3 MET I 58 ALA I 59 1 O MET I 58 N ALA E 59 SHEET 1 AA2 3 LYS G 65 ALA G 66 0 SHEET 2 AA2 3 LYS E 65 ALA E 66 1 N ALA E 66 O LYS G 65 SHEET 3 AA2 3 LYS I 65 ALA I 66 1 O ALA I 66 N LYS E 65 SHEET 1 AA3 3 MET M 58 ALA M 59 0 SHEET 2 AA3 3 MET K 58 ALA K 59 1 N MET K 58 O ALA M 59 SHEET 3 AA3 3 MET O 58 ALA O 59 1 O MET O 58 N ALA K 59 SHEET 1 AA4 3 LYS M 65 ALA M 66 0 SHEET 2 AA4 3 LYS K 65 ALA K 66 1 N ALA K 66 O LYS M 65 SHEET 3 AA4 3 LYS O 65 ALA O 66 1 O ALA O 66 N LYS K 65 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 179 VAL E 67 TER 319 GLU F 69 TER 498 VAL G 67 TER 638 GLU H 69 TER 817 VAL I 67 TER 957 GLU J 69 TER 1136 VAL K 67 TER 1276 GLU L 69 TER 1455 VAL M 67 TER 1595 GLU N 69 TER 1774 VAL O 67 TER 1914 GLU P 69 MASTER 201 0 0 0 12 0 0 6 1902 12 0 36 END