HEADER MEMBRANE PROTEIN 25-MAR-23 8IUX TITLE THE CRYOEM STRUCTURE OF H7N9-HA PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMAGGLUTININ; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: H7N9 SUBTYPE; SOURCE 3 ORGANISM_TAXID: 333278; SOURCE 4 GENE: HA; SOURCE 5 EXPRESSION_SYSTEM: BACULOVIRUS EXPRESSION VECTOR PFASTBAC1-HM; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 274590; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: HIGH FIVE CELL; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PFASTBAC 1-H7-HA KEYWDS H7N9, HA, TRIMER, COMPLEX, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR B.B.ZHAO,Z.Z.SUN REVDAT 1 24-APR-24 8IUX 0 JRNL AUTH B.B.ZHAO,Z.Z.SUN JRNL TITL THE CRYOEM STRUCTURE OF H7N9-HA PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 61557 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 8IUX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-APR-23. REMARK 100 THE DEPOSITION ID IS D_1300036506. 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 : CELL REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : HIGH FIVE CELL 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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) : 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C3). 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 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 -0.500000 -0.866024 -0.001782 508.36713 REMARK 350 BIOMT2 2 0.866025 -0.499997 -0.001801 136.58951 REMARK 350 BIOMT3 2 0.000669 -0.002444 0.999997 0.38194 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000669 135.89323 REMARK 350 BIOMT2 3 -0.866024 -0.499997 -0.002444 508.55325 REMARK 350 BIOMT3 3 -0.001782 -0.001801 0.999997 0.77005 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 VAL A 318 REMARK 465 PRO A 319 REMARK 465 LYS A 320 REMARK 465 GLY A 321 REMARK 465 LYS A 322 REMARK 465 ARG A 323 REMARK 465 THR A 324 REMARK 465 ALA A 325 REMARK 465 ARG A 326 REMARK 465 GLY A 327 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 PRO A 40 46.30 -79.43 REMARK 500 SER A 74 115.63 -160.19 REMARK 500 ASN A 124 37.25 -96.39 REMARK 500 ASN A 216 47.34 33.06 REMARK 500 ILE A 289 -60.24 -106.69 REMARK 500 GLN A 353 116.09 -160.78 REMARK 500 GLU A 398 75.18 45.76 REMARK 500 LEU A 452 58.95 -99.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 397 GLU A 398 134.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-35729 RELATED DB: EMDB REMARK 900 THE CRYOEM STRUCTURE OF H7N9-HA PROTEIN DBREF1 8IUX A 2 495 UNP A0A2D0Z8H0_9INFA DBREF2 8IUX A A0A2D0Z8H0 19 512 SEQRES 1 A 494 ASP LYS ILE CYS LEU GLY HIS HIS ALA VAL SER ASN GLY SEQRES 2 A 494 THR LYS VAL ASN THR LEU THR GLU ARG GLY VAL GLU VAL SEQRES 3 A 494 VAL ASN ALA THR GLU THR VAL GLU ARG THR ASN THR PRO SEQRES 4 A 494 ARG ILE CYS SER LYS GLY LYS ARG THR VAL ASP LEU GLY SEQRES 5 A 494 GLN CYS GLY LEU LEU GLY THR ILE THR GLY PRO PRO GLN SEQRES 6 A 494 CYS ASP GLN PHE LEU GLU PHE SER ALA ASP LEU ILE ILE SEQRES 7 A 494 GLU ARG ARG GLU GLY SER ASP VAL CYS TYR PRO GLY LYS SEQRES 8 A 494 PHE VAL ASN GLU GLU ALA LEU ARG GLN ILE LEU ARG GLU SEQRES 9 A 494 SER GLY GLY ILE ASP LYS GLU SER MET GLY PHE THR TYR SEQRES 10 A 494 ASN GLY ILE ARG THR ASN GLY VAL THR SER ALA CYS ARG SEQRES 11 A 494 ARG SER GLY SER SER PHE TYR ALA GLU MET LYS TRP LEU SEQRES 12 A 494 LEU SER ASN THR ASP ASN ALA ALA PHE PRO GLN MET THR SEQRES 13 A 494 LYS SER TYR LYS ASN THR ARG GLU SER PRO ALA ILE ILE SEQRES 14 A 494 VAL TRP GLY ILE HIS HIS SER VAL SER THR ALA GLU GLN SEQRES 15 A 494 THR LYS LEU TYR GLY SER GLY ASN LYS LEU VAL THR VAL SEQRES 16 A 494 GLY SER SER ASN TYR GLN GLN SER PHE VAL PRO SER PRO SEQRES 17 A 494 GLY ALA ARG PRO GLN VAL ASN GLY LEU SER GLY ARG ILE SEQRES 18 A 494 ASP PHE HIS TRP LEU ILE LEU ASN PRO ASN ASP THR VAL SEQRES 19 A 494 THR PHE SER PHE ASN GLY ALA PHE ILE ALA PRO ASP ARG SEQRES 20 A 494 ALA SER PHE LEU ARG GLY LYS SER MET GLY ILE GLN SER SEQRES 21 A 494 GLY VAL GLN VAL ASP ALA ASN CYS GLU GLY ASP CYS TYR SEQRES 22 A 494 HIS SER GLY GLY THR ILE ILE SER ASN LEU PRO PHE GLN SEQRES 23 A 494 ASN ILE ASP SER ARG ALA VAL GLY LYS CYS PRO ARG TYR SEQRES 24 A 494 VAL LYS GLN ARG SER LEU LEU LEU ALA THR GLY MET LYS SEQRES 25 A 494 ASN VAL PRO GLU VAL PRO LYS GLY LYS ARG THR ALA ARG SEQRES 26 A 494 GLY LEU PHE GLY ALA ILE ALA GLY PHE ILE GLU ASN GLY SEQRES 27 A 494 TRP GLU GLY LEU ILE ASP GLY TRP TYR GLY PHE ARG HIS SEQRES 28 A 494 GLN ASN ALA GLN GLY GLU GLY THR ALA ALA ASP TYR LYS SEQRES 29 A 494 SER THR GLN SER ALA ILE ASP GLN ILE THR GLY LYS LEU SEQRES 30 A 494 ASN ARG LEU ILE ALA LYS THR ASN GLN GLN PHE LYS LEU SEQRES 31 A 494 ILE ASP ASN GLU PHE ASN GLU VAL GLU LYS GLN ILE GLY SEQRES 32 A 494 ASN VAL ILE ASN TRP THR ARG ASP SER ILE THR GLU VAL SEQRES 33 A 494 TRP SER TYR ASN ALA GLU LEU LEU VAL ALA MET GLU ASN SEQRES 34 A 494 GLN HIS THR ILE ASP LEU ALA ASP SER GLU MET ASP LYS SEQRES 35 A 494 LEU TYR GLU ARG VAL LYS ARG GLN LEU ARG GLU ASN ALA SEQRES 36 A 494 GLU GLU ASP GLY THR GLY CYS PHE GLU ILE PHE HIS LYS SEQRES 37 A 494 CYS ASP ASP ASP CYS MET ALA SER ILE ARG ASN ASN THR SEQRES 38 A 494 TYR ASP HIS ARG LYS TYR ARG GLU GLU ALA MET GLN ASN HET NAG A 501 14 HET NAG A 502 14 HET NAG A 503 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG 3(C8 H15 N O6) HELIX 1 AA1 ASN A 95 GLU A 105 1 11 HELIX 2 AA2 SER A 179 TYR A 187 1 9 HELIX 3 AA3 ASP A 363 ILE A 382 1 20 HELIX 4 AA4 GLU A 400 LEU A 452 1 53 HELIX 5 AA5 ASP A 471 ASN A 480 1 10 HELIX 6 AA6 TYR A 488 MET A 493 1 6 SHEET 1 AA1 5 GLY A 357 THR A 360 0 SHEET 2 AA1 5 TYR A 348 ASN A 354 -1 N ASN A 354 O GLY A 357 SHEET 3 AA1 5 LYS A 3 HIS A 8 -1 N GLY A 7 O GLY A 349 SHEET 4 AA1 5 CYS A 463 ILE A 466 -1 O PHE A 464 N ILE A 4 SHEET 5 AA1 5 ALA A 456 GLU A 458 -1 N GLU A 457 O GLU A 465 SHEET 1 AA2 2 THR A 15 VAL A 17 0 SHEET 2 AA2 2 VAL A 25 VAL A 27 -1 O VAL A 25 N VAL A 17 SHEET 1 AA3 2 ALA A 30 GLU A 32 0 SHEET 2 AA3 2 LEU A 307 ALA A 309 -1 O LEU A 308 N THR A 31 SHEET 1 AA4 3 VAL A 34 GLU A 35 0 SHEET 2 AA4 3 PHE A 286 GLN A 287 1 O PHE A 286 N GLU A 35 SHEET 3 AA4 3 ARG A 299 TYR A 300 1 O ARG A 299 N GLN A 287 SHEET 1 AA5 2 ILE A 42 CYS A 43 0 SHEET 2 AA5 2 VAL A 265 ASP A 266 1 O ASP A 266 N ILE A 42 SHEET 1 AA6 3 THR A 49 ASP A 51 0 SHEET 2 AA6 3 LEU A 77 GLU A 80 1 O LEU A 77 N VAL A 50 SHEET 3 AA6 3 MET A 257 GLN A 260 1 O ILE A 259 N ILE A 78 SHEET 1 AA7 5 GLY A 91 PHE A 93 0 SHEET 2 AA7 5 ARG A 221 LEU A 229 1 O PHE A 224 N LYS A 92 SHEET 3 AA7 5 ALA A 168 HIS A 176 -1 N HIS A 176 O ARG A 221 SHEET 4 AA7 5 PHE A 243 PRO A 246 -1 O ILE A 244 N GLY A 173 SHEET 5 AA7 5 MET A 141 LEU A 144 -1 N LYS A 142 O ALA A 245 SHEET 1 AA8 2 ASP A 110 SER A 113 0 SHEET 2 AA8 2 ARG A 248 PHE A 251 -1 O ALA A 249 N GLU A 112 SHEET 1 AA9 3 MET A 156 LYS A 161 0 SHEET 2 AA9 3 THR A 234 PHE A 239 -1 O PHE A 239 N MET A 156 SHEET 3 AA9 3 VAL A 194 GLY A 197 -1 N GLY A 197 O THR A 236 SHEET 1 AB1 3 GLY A 278 THR A 279 0 SHEET 2 AB1 3 CYS A 273 HIS A 275 -1 N HIS A 275 O GLY A 278 SHEET 3 AB1 3 VAL A 294 GLY A 295 -1 O VAL A 294 N TYR A 274 SSBOND 1 CYS A 5 CYS A 463 1555 1555 2.03 SSBOND 2 CYS A 43 CYS A 269 1555 1555 2.03 SSBOND 3 CYS A 55 CYS A 67 1555 1555 2.03 SSBOND 4 CYS A 88 CYS A 130 1555 1555 2.03 SSBOND 5 CYS A 273 CYS A 297 1555 1555 2.03 SSBOND 6 CYS A 470 CYS A 474 1555 1555 2.03 LINK ND2 ASN A 29 C1 NAG A 502 1555 1555 1.44 LINK ND2 ASN A 408 C1 NAG A 501 1555 1555 1.44 LINK ND2 ASN A 480 C1 NAG A 503 1555 1555 1.45 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