HEADER SIGNALING PROTEIN 25-JUL-20 7JJC TITLE CRYSTAL STRUCTURE OF NEUROPILIN-1 B1 DOMAIN IN COMPLEX WITH SARS-COV-2 TITLE 2 S1 C-END RULE (CENDR) PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPILIN-1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: VASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SPIKE PROTEIN S1; COMPND 8 CHAIN: E, F, G, H; COMPND 9 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN,SPIKE GLYCOPROTEIN; COMPND 10 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: NRP1, NRP, VEGF165R; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA-GAMI 2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 14 2; SOURCE 15 ORGANISM_COMMON: 2019-NCOV; SOURCE 16 ORGANISM_TAXID: 2697049 KEYWDS NEUROPILIN-1, RECEPTOR BINDING, CORONAVIRUS, SARS-COV-2, SPIKE KEYWDS 2 PROTEIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.-E.CHEN,B.M.COLLINS REVDAT 4 18-OCT-23 7JJC 1 REMARK REVDAT 3 27-JAN-21 7JJC 1 COMPND REVDAT 2 25-NOV-20 7JJC 1 JRNL REVDAT 1 28-OCT-20 7JJC 0 JRNL AUTH J.L.DALY,B.SIMONETTI,K.KLEIN,K.E.CHEN,M.K.WILLIAMSON, JRNL AUTH 2 C.ANTON-PLAGARO,D.K.SHOEMARK,L.SIMON-GRACIA,M.BAUER, JRNL AUTH 3 R.HOLLANDI,U.F.GREBER,P.HORVATH,R.B.SESSIONS,A.HELENIUS, JRNL AUTH 4 J.A.HISCOX,T.TEESALU,D.A.MATTHEWS,A.D.DAVIDSON,B.M.COLLINS, JRNL AUTH 5 P.J.CULLEN,Y.YAMAUCHI JRNL TITL NEUROPILIN-1 IS A HOST FACTOR FOR SARS-COV-2 INFECTION. JRNL REF SCIENCE V. 370 861 2020 JRNL REFN ESSN 1095-9203 JRNL PMID 33082294 JRNL DOI 10.1126/SCIENCE.ABD3072 REMARK 2 REMARK 2 RESOLUTION. 2.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 36660 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.052 REMARK 3 FREE R VALUE TEST SET COUNT : 1852 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 5.5437 - 4.4013 1.00 2742 145 0.1383 0.1979 REMARK 3 2 4.4013 - 3.8453 1.00 2698 163 0.1705 0.1913 REMARK 3 3 3.8453 - 3.4938 1.00 2706 133 0.1947 0.2494 REMARK 3 4 3.4938 - 3.2435 1.00 2675 154 0.2187 0.2711 REMARK 3 5 3.2435 - 3.0523 1.00 2663 155 0.2296 0.3019 REMARK 3 6 3.0523 - 2.8994 1.00 2660 141 0.2487 0.2913 REMARK 3 7 2.8994 - 2.7733 1.00 2670 143 0.2619 0.3041 REMARK 3 8 2.7733 - 2.6665 1.00 2640 151 0.2600 0.3378 REMARK 3 9 2.6665 - 2.5745 1.00 2625 150 0.2685 0.3577 REMARK 3 10 2.5745 - 2.4940 1.00 2642 139 0.2889 0.3333 REMARK 3 11 2.4940 - 2.4227 1.00 2677 116 0.2959 0.3737 REMARK 3 12 2.4227 - 2.3600 0.95 2541 112 0.3182 0.3541 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.783 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 5532 REMARK 3 ANGLE : 0.709 7480 REMARK 3 CHIRALITY : 0.053 794 REMARK 3 PLANARITY : 0.004 952 REMARK 3 DIHEDRAL : 19.335 2070 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7JJC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250885. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 - 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95372 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36732 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.360 REMARK 200 RESOLUTION RANGE LOW (A) : 46.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 1.47800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: 1KEX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE PH 5, 20% PEG 6K, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 44.96500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.15000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.94500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.15000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.96500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.94500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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, E 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, G 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 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, H 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 GLY A -10 REMARK 465 SER A -9 REMARK 465 GLU A -8 REMARK 465 ASN A -7 REMARK 465 LEU A -6 REMARK 465 TYR A -5 REMARK 465 GLN A -4 REMARK 465 GLY C -10 REMARK 465 SER C -9 REMARK 465 GLU C -8 REMARK 465 ASN C -7 REMARK 465 LEU C -6 REMARK 465 TYR C -5 REMARK 465 GLN C -4 REMARK 465 ASN E 679 REMARK 465 SER E 680 REMARK 465 PRO E 681 REMARK 465 ARG E 682 REMARK 465 ASN F 679 REMARK 465 SER F 680 REMARK 465 PRO F 681 REMARK 465 ARG F 682 REMARK 465 ASN H 679 REMARK 465 SER H 680 REMARK 465 PRO H 681 REMARK 465 ARG H 682 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 312 CG REMARK 470 GLU A 319 CD OE1 OE2 REMARK 470 ARG A 323 CD NE REMARK 470 LYS A 347 CG CD CE NZ REMARK 470 GLU A 348 CD OE1 OE2 REMARK 470 LYS A 350 CG CD CE NZ REMARK 470 LYS A 359 NZ REMARK 470 LYS A 373 CG CD CE NZ REMARK 470 GLU A 374 CD OE1 OE2 REMARK 470 LYS A 377 CD CE NZ REMARK 470 LYS B 347 CD CE NZ REMARK 470 GLU B 348 CD OE1 OE2 REMARK 470 LYS B 359 NZ REMARK 470 LYS B 377 CG CD CE NZ REMARK 470 GLU C 304 CD OE1 OE2 REMARK 470 ARG C 323 CZ NH1 NH2 REMARK 470 LYS C 347 CE NZ REMARK 470 GLU C 348 CD OE1 OE2 REMARK 470 LYS C 350 CE NZ REMARK 470 LYS C 351 NZ REMARK 470 LYS C 359 NZ REMARK 470 LYS C 373 CE NZ REMARK 470 GLU C 374 CD OE1 OE2 REMARK 470 LYS C 377 CG CD CE NZ REMARK 470 GLU D 285 CD OE1 OE2 REMARK 470 LYS D 347 CG CD CE NZ REMARK 470 GLU D 348 CD OE1 OE2 REMARK 470 LYS D 350 CG CD CE NZ REMARK 470 LYS D 351 CD CE NZ REMARK 470 LYS D 359 NZ REMARK 470 LYS D 373 CE NZ REMARK 470 LYS D 377 CG CD CE NZ REMARK 470 ARG E 683 CD NE CZ NH1 NH2 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 ASN A 313 -148.02 62.58 REMARK 500 THR A 349 -11.38 -155.28 REMARK 500 ASN A 376 -3.63 78.63 REMARK 500 THR A 413 -57.02 64.35 REMARK 500 MET B 0 -126.98 -70.99 REMARK 500 PHE B 273 -49.93 -178.46 REMARK 500 ASN B 313 -154.48 61.39 REMARK 500 ASN B 376 -16.53 78.97 REMARK 500 ARG B 402 -36.40 -136.72 REMARK 500 THR B 413 -73.92 68.72 REMARK 500 ASN C 313 -150.72 64.16 REMARK 500 ASN C 376 -10.23 77.98 REMARK 500 THR C 413 -28.67 64.03 REMARK 500 SER D -9 -47.53 73.09 REMARK 500 SER D -9 -46.57 72.23 REMARK 500 ASN D 313 -161.54 57.44 REMARK 500 ARG D 323 -17.50 99.15 REMARK 500 THR D 413 -38.16 64.49 REMARK 500 ARG G 682 -90.20 -59.82 REMARK 500 ARG G 683 152.03 166.94 REMARK 500 ALA H 684 -84.33 -174.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 634 DISTANCE = 8.68 ANGSTROMS REMARK 525 HOH A 636 DISTANCE = 6.81 ANGSTROMS REMARK 525 HOH A 637 DISTANCE = 7.54 ANGSTROMS REMARK 525 HOH C 631 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH D 635 DISTANCE = 6.70 ANGSTROMS DBREF 7JJC A 273 427 UNP O14786 NRP1_HUMAN 273 427 DBREF 7JJC B 273 427 UNP O14786 NRP1_HUMAN 273 427 DBREF 7JJC C 273 427 UNP O14786 NRP1_HUMAN 273 427 DBREF 7JJC D 273 427 UNP O14786 NRP1_HUMAN 273 427 DBREF 7JJC E 679 685 UNP P0DTC2 SPIKE_SARS2 679 685 DBREF 7JJC F 679 685 UNP P0DTC2 SPIKE_SARS2 679 685 DBREF 7JJC G 679 685 UNP P0DTC2 SPIKE_SARS2 679 685 DBREF 7JJC H 679 685 UNP P0DTC2 SPIKE_SARS2 679 685 SEQADV 7JJC GLY A -10 UNP O14786 EXPRESSION TAG SEQADV 7JJC SER A -9 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLU A -8 UNP O14786 EXPRESSION TAG SEQADV 7JJC ASN A -7 UNP O14786 EXPRESSION TAG SEQADV 7JJC LEU A -6 UNP O14786 EXPRESSION TAG SEQADV 7JJC TYR A -5 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLN A -4 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLY A -3 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLY A -2 UNP O14786 EXPRESSION TAG SEQADV 7JJC HIS A -1 UNP O14786 EXPRESSION TAG SEQADV 7JJC MET A 0 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLY B -10 UNP O14786 EXPRESSION TAG SEQADV 7JJC SER B -9 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLU B -8 UNP O14786 EXPRESSION TAG SEQADV 7JJC ASN B -7 UNP O14786 EXPRESSION TAG SEQADV 7JJC LEU B -6 UNP O14786 EXPRESSION TAG SEQADV 7JJC TYR B -5 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLN B -4 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLY B -3 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLY B -2 UNP O14786 EXPRESSION TAG SEQADV 7JJC HIS B -1 UNP O14786 EXPRESSION TAG SEQADV 7JJC MET B 0 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLY C -10 UNP O14786 EXPRESSION TAG SEQADV 7JJC SER C -9 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLU C -8 UNP O14786 EXPRESSION TAG SEQADV 7JJC ASN C -7 UNP O14786 EXPRESSION TAG SEQADV 7JJC LEU C -6 UNP O14786 EXPRESSION TAG SEQADV 7JJC TYR C -5 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLN C -4 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLY C -3 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLY C -2 UNP O14786 EXPRESSION TAG SEQADV 7JJC HIS C -1 UNP O14786 EXPRESSION TAG SEQADV 7JJC MET C 0 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLY D -10 UNP O14786 EXPRESSION TAG SEQADV 7JJC SER D -9 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLU D -8 UNP O14786 EXPRESSION TAG SEQADV 7JJC ASN D -7 UNP O14786 EXPRESSION TAG SEQADV 7JJC LEU D -6 UNP O14786 EXPRESSION TAG SEQADV 7JJC TYR D -5 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLN D -4 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLY D -3 UNP O14786 EXPRESSION TAG SEQADV 7JJC GLY D -2 UNP O14786 EXPRESSION TAG SEQADV 7JJC HIS D -1 UNP O14786 EXPRESSION TAG SEQADV 7JJC MET D 0 UNP O14786 EXPRESSION TAG SEQRES 1 A 166 GLY SER GLU ASN LEU TYR GLN GLY GLY HIS MET PHE LYS SEQRES 2 A 166 CYS MET GLU ALA LEU GLY MET GLU SER GLY GLU ILE HIS SEQRES 3 A 166 SER ASP GLN ILE THR ALA SER SER GLN TYR SER THR ASN SEQRES 4 A 166 TRP SER ALA GLU ARG SER ARG LEU ASN TYR PRO GLU ASN SEQRES 5 A 166 GLY TRP THR PRO GLY GLU ASP SER TYR ARG GLU TRP ILE SEQRES 6 A 166 GLN VAL ASP LEU GLY LEU LEU ARG PHE VAL THR ALA VAL SEQRES 7 A 166 GLY THR GLN GLY ALA ILE SER LYS GLU THR LYS LYS LYS SEQRES 8 A 166 TYR TYR VAL LYS THR TYR LYS ILE ASP VAL SER SER ASN SEQRES 9 A 166 GLY GLU ASP TRP ILE THR ILE LYS GLU GLY ASN LYS PRO SEQRES 10 A 166 VAL LEU PHE GLN GLY ASN THR ASN PRO THR ASP VAL VAL SEQRES 11 A 166 VAL ALA VAL PHE PRO LYS PRO LEU ILE THR ARG PHE VAL SEQRES 12 A 166 ARG ILE LYS PRO ALA THR TRP GLU THR GLY ILE SER MET SEQRES 13 A 166 ARG PHE GLU VAL TYR GLY CYS LYS ILE THR SEQRES 1 B 166 GLY SER GLU ASN LEU TYR GLN GLY GLY HIS MET PHE LYS SEQRES 2 B 166 CYS MET GLU ALA LEU GLY MET GLU SER GLY GLU ILE HIS SEQRES 3 B 166 SER ASP GLN ILE THR ALA SER SER GLN TYR SER THR ASN SEQRES 4 B 166 TRP SER ALA GLU ARG SER ARG LEU ASN TYR PRO GLU ASN SEQRES 5 B 166 GLY TRP THR PRO GLY GLU ASP SER TYR ARG GLU TRP ILE SEQRES 6 B 166 GLN VAL ASP LEU GLY LEU LEU ARG PHE VAL THR ALA VAL SEQRES 7 B 166 GLY THR GLN GLY ALA ILE SER LYS GLU THR LYS LYS LYS SEQRES 8 B 166 TYR TYR VAL LYS THR TYR LYS ILE ASP VAL SER SER ASN SEQRES 9 B 166 GLY GLU ASP TRP ILE THR ILE LYS GLU GLY ASN LYS PRO SEQRES 10 B 166 VAL LEU PHE GLN GLY ASN THR ASN PRO THR ASP VAL VAL SEQRES 11 B 166 VAL ALA VAL PHE PRO LYS PRO LEU ILE THR ARG PHE VAL SEQRES 12 B 166 ARG ILE LYS PRO ALA THR TRP GLU THR GLY ILE SER MET SEQRES 13 B 166 ARG PHE GLU VAL TYR GLY CYS LYS ILE THR SEQRES 1 C 166 GLY SER GLU ASN LEU TYR GLN GLY GLY HIS MET PHE LYS SEQRES 2 C 166 CYS MET GLU ALA LEU GLY MET GLU SER GLY GLU ILE HIS SEQRES 3 C 166 SER ASP GLN ILE THR ALA SER SER GLN TYR SER THR ASN SEQRES 4 C 166 TRP SER ALA GLU ARG SER ARG LEU ASN TYR PRO GLU ASN SEQRES 5 C 166 GLY TRP THR PRO GLY GLU ASP SER TYR ARG GLU TRP ILE SEQRES 6 C 166 GLN VAL ASP LEU GLY LEU LEU ARG PHE VAL THR ALA VAL SEQRES 7 C 166 GLY THR GLN GLY ALA ILE SER LYS GLU THR LYS LYS LYS SEQRES 8 C 166 TYR TYR VAL LYS THR TYR LYS ILE ASP VAL SER SER ASN SEQRES 9 C 166 GLY GLU ASP TRP ILE THR ILE LYS GLU GLY ASN LYS PRO SEQRES 10 C 166 VAL LEU PHE GLN GLY ASN THR ASN PRO THR ASP VAL VAL SEQRES 11 C 166 VAL ALA VAL PHE PRO LYS PRO LEU ILE THR ARG PHE VAL SEQRES 12 C 166 ARG ILE LYS PRO ALA THR TRP GLU THR GLY ILE SER MET SEQRES 13 C 166 ARG PHE GLU VAL TYR GLY CYS LYS ILE THR SEQRES 1 D 166 GLY SER GLU ASN LEU TYR GLN GLY GLY HIS MET PHE LYS SEQRES 2 D 166 CYS MET GLU ALA LEU GLY MET GLU SER GLY GLU ILE HIS SEQRES 3 D 166 SER ASP GLN ILE THR ALA SER SER GLN TYR SER THR ASN SEQRES 4 D 166 TRP SER ALA GLU ARG SER ARG LEU ASN TYR PRO GLU ASN SEQRES 5 D 166 GLY TRP THR PRO GLY GLU ASP SER TYR ARG GLU TRP ILE SEQRES 6 D 166 GLN VAL ASP LEU GLY LEU LEU ARG PHE VAL THR ALA VAL SEQRES 7 D 166 GLY THR GLN GLY ALA ILE SER LYS GLU THR LYS LYS LYS SEQRES 8 D 166 TYR TYR VAL LYS THR TYR LYS ILE ASP VAL SER SER ASN SEQRES 9 D 166 GLY GLU ASP TRP ILE THR ILE LYS GLU GLY ASN LYS PRO SEQRES 10 D 166 VAL LEU PHE GLN GLY ASN THR ASN PRO THR ASP VAL VAL SEQRES 11 D 166 VAL ALA VAL PHE PRO LYS PRO LEU ILE THR ARG PHE VAL SEQRES 12 D 166 ARG ILE LYS PRO ALA THR TRP GLU THR GLY ILE SER MET SEQRES 13 D 166 ARG PHE GLU VAL TYR GLY CYS LYS ILE THR SEQRES 1 E 7 ASN SER PRO ARG ARG ALA ARG SEQRES 1 F 7 ASN SER PRO ARG ARG ALA ARG SEQRES 1 G 7 ASN SER PRO ARG ARG ALA ARG SEQRES 1 H 7 ASN SER PRO ARG ARG ALA ARG HET PEG A 501 7 HET PEG B 501 7 HET PEG C 501 7 HET GOL C 502 6 HET GOL C 503 6 HET PEG D 501 7 HET GOL D 502 6 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 9 PEG 4(C4 H10 O3) FORMUL 12 GOL 3(C3 H8 O3) FORMUL 16 HOH *128(H2 O) HELIX 1 AA1 HIS A 287 ASP A 289 5 3 HELIX 2 AA2 SER A 298 ARG A 307 5 10 HELIX 3 AA3 GLN B -4 MET B 0 5 5 HELIX 4 AA4 HIS B 287 ASP B 289 5 3 HELIX 5 AA5 SER B 298 SER B 306 5 9 HELIX 6 AA6 HIS C 287 ASP C 289 5 3 HELIX 7 AA7 SER C 298 ARG C 307 5 10 HELIX 8 AA8 GLN D -4 MET D 0 5 5 HELIX 9 AA9 HIS D 287 ASP D 289 5 3 HELIX 10 AB1 SER D 298 ARG D 307 5 10 SHEET 1 AA1 3 ALA A 344 ILE A 345 0 SHEET 2 AA1 3 LYS A 352 SER A 363 -1 O TYR A 353 N ALA A 344 SHEET 3 AA1 3 ILE A 370 THR A 371 -1 O ILE A 370 N VAL A 362 SHEET 1 AA2 5 PHE A 381 GLN A 382 0 SHEET 2 AA2 5 LYS A 352 SER A 363 -1 N TYR A 358 O PHE A 381 SHEET 3 AA2 5 VAL A 391 GLU A 412 -1 O ARG A 405 N ASP A 361 SHEET 4 AA2 5 ILE A 326 GLN A 342 -1 N VAL A 336 O LEU A 399 SHEET 5 AA2 5 ILE A 291 ALA A 293 -1 N THR A 292 O GLN A 327 SHEET 1 AA3 7 ILE A 291 ALA A 293 0 SHEET 2 AA3 7 ILE A 326 GLN A 342 -1 O GLN A 327 N THR A 292 SHEET 3 AA3 7 ARG A 418 THR A 427 -1 O TYR A 422 N THR A 337 SHEET 4 AA3 7 MET A 0 ALA A 278 -1 N GLU A 277 O GLY A 423 SHEET 5 AA3 7 VAL B 391 GLU B 412 -1 O PRO B 398 N CYS A 275 SHEET 6 AA3 7 LYS B 352 SER B 363 -1 N ASP B 361 O ARG B 405 SHEET 7 AA3 7 ILE B 370 THR B 371 -1 O ILE B 370 N VAL B 362 SHEET 1 AA4 3 ALA B 344 ILE B 345 0 SHEET 2 AA4 3 LYS B 352 SER B 363 -1 O TYR B 353 N ALA B 344 SHEET 3 AA4 3 PHE B 381 GLN B 382 -1 O PHE B 381 N TYR B 358 SHEET 1 AA5 5 PHE B 381 GLN B 382 0 SHEET 2 AA5 5 LYS B 352 SER B 363 -1 N TYR B 358 O PHE B 381 SHEET 3 AA5 5 VAL B 391 GLU B 412 -1 O ARG B 405 N ASP B 361 SHEET 4 AA5 5 ILE B 326 GLN B 342 -1 N VAL B 339 O ALA B 393 SHEET 5 AA5 5 ILE B 291 ALA B 293 -1 N THR B 292 O GLN B 327 SHEET 1 AA6 4 ILE B 291 ALA B 293 0 SHEET 2 AA6 4 ILE B 326 GLN B 342 -1 O GLN B 327 N THR B 292 SHEET 3 AA6 4 ARG B 418 CYS B 424 -1 O TYR B 422 N ALA B 338 SHEET 4 AA6 4 GLU B 277 ALA B 278 -1 N GLU B 277 O GLY B 423 SHEET 1 AA7 2 LYS B 373 GLU B 374 0 SHEET 2 AA7 2 LYS B 377 PRO B 378 -1 O LYS B 377 N GLU B 374 SHEET 1 AA8 3 ALA C 344 ILE C 345 0 SHEET 2 AA8 3 LYS C 352 SER C 363 -1 O TYR C 353 N ALA C 344 SHEET 3 AA8 3 ILE C 370 THR C 371 -1 O ILE C 370 N VAL C 362 SHEET 1 AA9 5 PHE C 381 GLN C 382 0 SHEET 2 AA9 5 LYS C 352 SER C 363 -1 N TYR C 358 O PHE C 381 SHEET 3 AA9 5 VAL C 391 GLU C 412 -1 O LYS C 407 N LYS C 359 SHEET 4 AA9 5 ILE C 326 GLN C 342 -1 N ILE C 326 O ILE C 406 SHEET 5 AA9 5 ILE C 291 ALA C 293 -1 N THR C 292 O GLN C 327 SHEET 1 AB1 7 ILE C 291 ALA C 293 0 SHEET 2 AB1 7 ILE C 326 GLN C 342 -1 O GLN C 327 N THR C 292 SHEET 3 AB1 7 ARG C 418 THR C 427 -1 O ARG C 418 N GLN C 342 SHEET 4 AB1 7 MET C 0 ALA C 278 -1 N GLU C 277 O GLY C 423 SHEET 5 AB1 7 VAL D 391 GLU D 412 -1 O PRO D 398 N CYS C 275 SHEET 6 AB1 7 LYS D 352 SER D 363 -1 N LYS D 359 O LYS D 407 SHEET 7 AB1 7 ILE D 370 THR D 371 -1 O ILE D 370 N VAL D 362 SHEET 1 AB2 3 ALA D 344 ILE D 345 0 SHEET 2 AB2 3 LYS D 352 SER D 363 -1 O TYR D 353 N ALA D 344 SHEET 3 AB2 3 PHE D 381 GLN D 382 -1 O PHE D 381 N TYR D 358 SHEET 1 AB3 5 PHE D 381 GLN D 382 0 SHEET 2 AB3 5 LYS D 352 SER D 363 -1 N TYR D 358 O PHE D 381 SHEET 3 AB3 5 VAL D 391 GLU D 412 -1 O LYS D 407 N LYS D 359 SHEET 4 AB3 5 ILE D 326 GLN D 342 -1 N VAL D 339 O ALA D 393 SHEET 5 AB3 5 ILE D 291 ALA D 293 -1 N THR D 292 O GLN D 327 SHEET 1 AB4 4 ILE D 291 ALA D 293 0 SHEET 2 AB4 4 ILE D 326 GLN D 342 -1 O GLN D 327 N THR D 292 SHEET 3 AB4 4 ARG D 418 CYS D 424 -1 O ARG D 418 N GLN D 342 SHEET 4 AB4 4 GLU D 277 ALA D 278 -1 N GLU D 277 O GLY D 423 SHEET 1 AB5 2 LYS C 373 GLU C 374 0 SHEET 2 AB5 2 LYS C 377 PRO C 378 -1 O LYS C 377 N GLU C 374 SHEET 1 AB6 2 LYS D 373 GLU D 374 0 SHEET 2 AB6 2 LYS D 377 PRO D 378 -1 O LYS D 377 N GLU D 374 SSBOND 1 CYS A 275 CYS A 424 1555 1555 2.04 SSBOND 2 CYS B 275 CYS B 424 1555 1555 2.03 SSBOND 3 CYS C 275 CYS C 424 1555 1555 2.03 SSBOND 4 CYS D 275 CYS D 424 1555 1555 2.03 CRYST1 89.930 89.890 108.300 90.00 90.00 90.00 P 21 21 21 16 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 0.011120 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011125 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009234 0.00000