HEADER IMMUNE SYSTEM 10-OCT-23 8UIP TITLE CRYO-EM STRUCTURE OF HUMAN NINJURIN1 CURVED OLIGOMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: NINJURIN-1; COMPND 3 CHAIN: A, B, C; COMPND 4 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: NINJ1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA PHAGE ECSZW_1; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 2419742 KEYWDS NINJURIN1, NINJ1, INFLAMMATION, INFLAMMASOME, PYROPTOSIS, PLASMA KEYWDS 2 MEMBRANE RUPTURE, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR L.DAVID,H.WU REVDAT 2 08-MAY-24 8UIP 1 JRNL REVDAT 1 01-MAY-24 8UIP 0 JRNL AUTH L.DAVID,J.P.BORGES,L.R.HOLLINGSWORTH,A.VOLCHUK,I.JANSEN, JRNL AUTH 2 E.GARLICK,B.E.STEINBERG,H.WU JRNL TITL NINJ1 MEDIATES PLASMA MEMBRANE RUPTURE BY CUTTING AND JRNL TITL 2 RELEASING MEMBRANE DISKS. JRNL REF CELL V. 187 2224 2024 JRNL REFN ISSN 1097-4172 JRNL PMID 38614101 JRNL DOI 10.1016/J.CELL.2024.03.008 REMARK 2 REMARK 2 RESOLUTION. 4.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERIALEM 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 : BACKBONE TRACE 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) : 4.300 REMARK 3 NUMBER OF PARTICLES : 626231 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 8UIP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1000278185. 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 : NINJURIN 1 RING OLIGOMER REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.50 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 5130.00 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA 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 1 REMARK 465 ASP A 2 REMARK 465 SER A 3 REMARK 465 GLY A 4 REMARK 465 THR A 5 REMARK 465 GLU A 6 REMARK 465 GLU A 7 REMARK 465 TYR A 8 REMARK 465 GLU A 9 REMARK 465 LEU A 10 REMARK 465 ASN A 11 REMARK 465 GLY A 12 REMARK 465 GLY A 13 REMARK 465 LEU A 14 REMARK 465 PRO A 15 REMARK 465 PRO A 16 REMARK 465 GLY A 17 REMARK 465 THR A 18 REMARK 465 PRO A 19 REMARK 465 GLY A 20 REMARK 465 SER A 21 REMARK 465 PRO A 22 REMARK 465 ASP A 23 REMARK 465 ALA A 24 REMARK 465 SER A 25 REMARK 465 PRO A 26 REMARK 465 ALA A 27 REMARK 465 ARG A 28 REMARK 465 TRP A 29 REMARK 465 GLY A 30 REMARK 465 TRP A 31 REMARK 465 ARG A 32 REMARK 465 HIS A 33 REMARK 465 GLY A 34 REMARK 465 PRO A 35 REMARK 465 ILE A 36 REMARK 465 ASN A 37 REMARK 465 VAL A 38 REMARK 465 GLY A 140 REMARK 465 VAL A 141 REMARK 465 GLN A 142 REMARK 465 LYS A 143 REMARK 465 PRO A 144 REMARK 465 LEU A 145 REMARK 465 MET A 146 REMARK 465 ASP A 147 REMARK 465 MET A 148 REMARK 465 ALA A 149 REMARK 465 PRO A 150 REMARK 465 GLN A 151 REMARK 465 GLN A 152 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 SER B 3 REMARK 465 GLY B 4 REMARK 465 THR B 5 REMARK 465 GLU B 6 REMARK 465 GLU B 7 REMARK 465 TYR B 8 REMARK 465 GLU B 9 REMARK 465 LEU B 10 REMARK 465 ASN B 11 REMARK 465 GLY B 12 REMARK 465 GLY B 13 REMARK 465 LEU B 14 REMARK 465 PRO B 15 REMARK 465 PRO B 16 REMARK 465 GLY B 17 REMARK 465 THR B 18 REMARK 465 PRO B 19 REMARK 465 GLY B 20 REMARK 465 SER B 21 REMARK 465 PRO B 22 REMARK 465 ASP B 23 REMARK 465 ALA B 24 REMARK 465 SER B 25 REMARK 465 PRO B 26 REMARK 465 ALA B 27 REMARK 465 ARG B 28 REMARK 465 TRP B 29 REMARK 465 GLY B 30 REMARK 465 TRP B 31 REMARK 465 ARG B 32 REMARK 465 HIS B 33 REMARK 465 GLY B 34 REMARK 465 PRO B 35 REMARK 465 ILE B 36 REMARK 465 ASN B 37 REMARK 465 VAL B 38 REMARK 465 GLY B 140 REMARK 465 VAL B 141 REMARK 465 GLN B 142 REMARK 465 LYS B 143 REMARK 465 PRO B 144 REMARK 465 LEU B 145 REMARK 465 MET B 146 REMARK 465 ASP B 147 REMARK 465 MET B 148 REMARK 465 ALA B 149 REMARK 465 PRO B 150 REMARK 465 GLN B 151 REMARK 465 GLN B 152 REMARK 465 MET C 1 REMARK 465 ASP C 2 REMARK 465 SER C 3 REMARK 465 GLY C 4 REMARK 465 THR C 5 REMARK 465 GLU C 6 REMARK 465 GLU C 7 REMARK 465 TYR C 8 REMARK 465 GLU C 9 REMARK 465 LEU C 10 REMARK 465 ASN C 11 REMARK 465 GLY C 12 REMARK 465 GLY C 13 REMARK 465 LEU C 14 REMARK 465 PRO C 15 REMARK 465 PRO C 16 REMARK 465 GLY C 17 REMARK 465 THR C 18 REMARK 465 PRO C 19 REMARK 465 GLY C 20 REMARK 465 SER C 21 REMARK 465 PRO C 22 REMARK 465 ASP C 23 REMARK 465 ALA C 24 REMARK 465 SER C 25 REMARK 465 PRO C 26 REMARK 465 ALA C 27 REMARK 465 ARG C 28 REMARK 465 TRP C 29 REMARK 465 GLY C 30 REMARK 465 TRP C 31 REMARK 465 ARG C 32 REMARK 465 HIS C 33 REMARK 465 GLY C 34 REMARK 465 PRO C 35 REMARK 465 ILE C 36 REMARK 465 ASN C 37 REMARK 465 VAL C 38 REMARK 465 GLY C 140 REMARK 465 VAL C 141 REMARK 465 GLN C 142 REMARK 465 LYS C 143 REMARK 465 PRO C 144 REMARK 465 LEU C 145 REMARK 465 MET C 146 REMARK 465 ASP C 147 REMARK 465 MET C 148 REMARK 465 ALA C 149 REMARK 465 PRO C 150 REMARK 465 GLN C 151 REMARK 465 GLN C 152 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 O ALA C 42 OG SER C 46 2.09 REMARK 500 O ALA A 42 OG SER A 46 2.09 REMARK 500 O ALA B 42 OG SER B 46 2.09 REMARK 500 O PHE B 117 ND2 ASN B 120 2.15 REMARK 500 O PHE A 117 ND2 ASN A 120 2.15 REMARK 500 O PHE C 117 ND2 ASN C 120 2.15 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 MET A 51 -16.21 71.44 REMARK 500 LEU A 52 138.25 -175.50 REMARK 500 PHE A 76 48.96 -97.79 REMARK 500 ASP A 105 11.59 58.57 REMARK 500 MET B 51 -16.14 71.41 REMARK 500 LEU B 52 138.30 -175.55 REMARK 500 PHE B 76 48.95 -97.74 REMARK 500 ASP B 105 11.60 58.58 REMARK 500 MET C 51 -16.21 71.46 REMARK 500 LEU C 52 138.33 -175.50 REMARK 500 PHE C 76 48.96 -97.78 REMARK 500 ASP C 105 11.54 58.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-42301 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN NINJURIN1 RING SEGMENT DBREF 8UIP A 1 152 UNP Q92982 NINJ1_HUMAN 1 152 DBREF 8UIP B 1 152 UNP Q92982 NINJ1_HUMAN 1 152 DBREF 8UIP C 1 152 UNP Q92982 NINJ1_HUMAN 1 152 SEQRES 1 A 152 MET ASP SER GLY THR GLU GLU TYR GLU LEU ASN GLY GLY SEQRES 2 A 152 LEU PRO PRO GLY THR PRO GLY SER PRO ASP ALA SER PRO SEQRES 3 A 152 ALA ARG TRP GLY TRP ARG HIS GLY PRO ILE ASN VAL ASN SEQRES 4 A 152 HIS TYR ALA SER LYS LYS SER ALA ALA GLU SER MET LEU SEQRES 5 A 152 ASP ILE ALA LEU LEU MET ALA ASN ALA SER GLN LEU LYS SEQRES 6 A 152 ALA VAL VAL GLU GLN GLY PRO SER PHE ALA PHE TYR VAL SEQRES 7 A 152 PRO LEU VAL VAL LEU ILE SER ILE SER LEU VAL LEU GLN SEQRES 8 A 152 ILE GLY VAL GLY VAL LEU LEU ILE PHE LEU VAL LYS TYR SEQRES 9 A 152 ASP LEU ASN ASN PRO ALA LYS HIS ALA LYS LEU ASP PHE SEQRES 10 A 152 LEU ASN ASN LEU ALA THR GLY LEU VAL PHE ILE ILE VAL SEQRES 11 A 152 VAL VAL ASN ILE PHE ILE THR ALA PHE GLY VAL GLN LYS SEQRES 12 A 152 PRO LEU MET ASP MET ALA PRO GLN GLN SEQRES 1 B 152 MET ASP SER GLY THR GLU GLU TYR GLU LEU ASN GLY GLY SEQRES 2 B 152 LEU PRO PRO GLY THR PRO GLY SER PRO ASP ALA SER PRO SEQRES 3 B 152 ALA ARG TRP GLY TRP ARG HIS GLY PRO ILE ASN VAL ASN SEQRES 4 B 152 HIS TYR ALA SER LYS LYS SER ALA ALA GLU SER MET LEU SEQRES 5 B 152 ASP ILE ALA LEU LEU MET ALA ASN ALA SER GLN LEU LYS SEQRES 6 B 152 ALA VAL VAL GLU GLN GLY PRO SER PHE ALA PHE TYR VAL SEQRES 7 B 152 PRO LEU VAL VAL LEU ILE SER ILE SER LEU VAL LEU GLN SEQRES 8 B 152 ILE GLY VAL GLY VAL LEU LEU ILE PHE LEU VAL LYS TYR SEQRES 9 B 152 ASP LEU ASN ASN PRO ALA LYS HIS ALA LYS LEU ASP PHE SEQRES 10 B 152 LEU ASN ASN LEU ALA THR GLY LEU VAL PHE ILE ILE VAL SEQRES 11 B 152 VAL VAL ASN ILE PHE ILE THR ALA PHE GLY VAL GLN LYS SEQRES 12 B 152 PRO LEU MET ASP MET ALA PRO GLN GLN SEQRES 1 C 152 MET ASP SER GLY THR GLU GLU TYR GLU LEU ASN GLY GLY SEQRES 2 C 152 LEU PRO PRO GLY THR PRO GLY SER PRO ASP ALA SER PRO SEQRES 3 C 152 ALA ARG TRP GLY TRP ARG HIS GLY PRO ILE ASN VAL ASN SEQRES 4 C 152 HIS TYR ALA SER LYS LYS SER ALA ALA GLU SER MET LEU SEQRES 5 C 152 ASP ILE ALA LEU LEU MET ALA ASN ALA SER GLN LEU LYS SEQRES 6 C 152 ALA VAL VAL GLU GLN GLY PRO SER PHE ALA PHE TYR VAL SEQRES 7 C 152 PRO LEU VAL VAL LEU ILE SER ILE SER LEU VAL LEU GLN SEQRES 8 C 152 ILE GLY VAL GLY VAL LEU LEU ILE PHE LEU VAL LYS TYR SEQRES 9 C 152 ASP LEU ASN ASN PRO ALA LYS HIS ALA LYS LEU ASP PHE SEQRES 10 C 152 LEU ASN ASN LEU ALA THR GLY LEU VAL PHE ILE ILE VAL SEQRES 11 C 152 VAL VAL ASN ILE PHE ILE THR ALA PHE GLY VAL GLN LYS SEQRES 12 C 152 PRO LEU MET ASP MET ALA PRO GLN GLN HELIX 1 AA1 SER A 43 GLU A 49 1 7 HELIX 2 AA2 ILE A 54 GLN A 70 1 17 HELIX 3 AA3 PRO A 79 PHE A 100 1 22 HELIX 4 AA4 ALA A 110 PHE A 139 1 30 HELIX 5 AA5 SER B 43 GLU B 49 1 7 HELIX 6 AA6 ILE B 54 GLN B 70 1 17 HELIX 7 AA7 PRO B 79 PHE B 100 1 22 HELIX 8 AA8 ALA B 110 PHE B 139 1 30 HELIX 9 AA9 SER C 43 GLU C 49 1 7 HELIX 10 AB1 ILE C 54 GLN C 70 1 17 HELIX 11 AB2 PRO C 79 PHE C 100 1 22 HELIX 12 AB3 ALA C 110 PHE C 139 1 30 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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