HEADER IMMUNE SYSTEM 01-OCT-23 8UEK TITLE SOLUTION STRUCTURE OF ACKR3-TARGETING NANOBODY VUN701 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACKR3-TARGETING NANOBODY VUN701; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_COMMON: LLAMA; SOURCE 4 ORGANISM_TAXID: 9844; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS ACKR3, GPCR, NANOBODY, VUN701, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.R.SCHLIMGEN,F.C.PETERSON,B.F.VOLKMAN REVDAT 1 12-JUN-24 8UEK 0 JRNL AUTH R.R.SCHLIMGEN,F.C.PETERSON,R.HEUKERS,M.J.SMIT,J.D.MCCORVY, JRNL AUTH 2 B.F.VOLKMAN JRNL TITL STRUCTURAL BASIS FOR SELECTIVITY AND ANTAGONISM IN JRNL TITL 2 EXTRACELLULAR GPCR-NANOBODIES. JRNL REF NAT COMMUN V. 15 4611 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38816420 JRNL DOI 10.1038/S41467-024-49000-X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.0 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8UEK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1000277905. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 25 MM [U-100% 2H] MES, 0.75 MM REMARK 210 [U-98% 13C; U-98% 15N] VUN701, REMARK 210 0.02 % V/V SODIUM AZIDE, 95% H2O/ REMARK 210 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCO REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.6, NMRPIPE 9.6, XEASY REMARK 210 1.3.13, GARANT 2.2, X-PLOR NIH, REMARK 210 CYANA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 ASP A 74 -2.97 -165.90 REMARK 500 2 ASP A 74 -43.81 -164.65 REMARK 500 2 ALA A 91 -178.50 -177.92 REMARK 500 2 ARG A 103 -49.98 -156.31 REMARK 500 3 ASP A 74 -23.45 -149.69 REMARK 500 3 ALA A 91 -169.55 -179.92 REMARK 500 4 ARG A 66 -73.61 -115.74 REMARK 500 4 ASP A 74 -22.87 -162.07 REMARK 500 4 ALA A 91 -175.94 -176.27 REMARK 500 4 ASP A 104 -23.29 -157.26 REMARK 500 5 ASP A 74 -5.11 -166.46 REMARK 500 6 ASP A 74 -24.05 -145.37 REMARK 500 6 ALA A 91 -175.96 -172.39 REMARK 500 7 ASP A 74 82.36 50.01 REMARK 500 7 LYS A 75 -30.63 177.54 REMARK 500 7 ALA A 91 -168.22 -169.88 REMARK 500 7 ASP A 104 -22.07 -159.50 REMARK 500 8 SER A 0 -77.05 -76.36 REMARK 500 8 ASP A 74 -32.76 -149.80 REMARK 500 8 ALA A 91 -178.28 -174.11 REMARK 500 8 ARG A 103 -40.90 -151.58 REMARK 500 9 SER A -2 -26.04 70.86 REMARK 500 9 ASP A 74 -37.19 -162.98 REMARK 500 9 ALA A 91 -176.65 -178.55 REMARK 500 10 SER A -2 -179.63 69.43 REMARK 500 10 ASP A 74 -43.41 -144.89 REMARK 500 10 THR A 77 -167.82 -107.65 REMARK 500 10 ALA A 91 -173.84 -171.56 REMARK 500 11 SER A -2 -172.41 64.09 REMARK 500 11 ARG A 66 -66.48 -94.00 REMARK 500 11 ASP A 74 -27.28 -141.55 REMARK 500 11 THR A 77 -72.98 -107.17 REMARK 500 11 VAL A 78 115.65 175.53 REMARK 500 11 ALA A 91 -172.89 -177.64 REMARK 500 11 ASP A 104 -21.52 -144.30 REMARK 500 12 ASP A 74 -54.56 -143.78 REMARK 500 12 ALA A 91 -171.28 -176.77 REMARK 500 12 ARG A 103 -40.96 69.39 REMARK 500 13 SER A -2 88.96 65.94 REMARK 500 13 SER A 0 -175.90 67.39 REMARK 500 13 ASP A 74 -19.48 -169.02 REMARK 500 13 ALA A 91 -174.91 -178.74 REMARK 500 13 ASP A 104 -19.71 -142.28 REMARK 500 14 SER A -2 80.18 68.18 REMARK 500 14 LYS A 75 9.16 102.25 REMARK 500 14 ALA A 91 -167.86 -172.54 REMARK 500 14 ARG A 103 -41.90 67.90 REMARK 500 15 SER A -2 -60.96 -152.73 REMARK 500 15 ASP A 74 -39.80 -154.73 REMARK 500 15 THR A 77 -165.34 -107.87 REMARK 500 REMARK 500 THIS ENTRY HAS 64 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31108 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF ACKR3-TARGETING NANOBODY VUN701 DBREF 8UEK A -3 120 PDB 8UEK 8UEK -3 120 SEQRES 1 A 124 GLY SER GLY SER GLN VAL GLN LEU VAL GLU SER GLY GLY SEQRES 2 A 124 GLY LEU VAL GLN ALA GLY GLY SER LEU ARG LEU SER CYS SEQRES 3 A 124 ALA ALA SER GLY SER THR PHE SER LEU HIS LEU MET GLY SEQRES 4 A 124 TRP TYR ARG GLN ALA PRO GLY LYS GLN ARG GLU VAL VAL SEQRES 5 A 124 ALA THR SER GLY SER GLY GLY ASP THR ASN TYR ALA ASP SEQRES 6 A 124 SER VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ASP SEQRES 7 A 124 LYS ASN THR VAL ASP LEU GLN MET ASN ASN LEU LYS PRO SEQRES 8 A 124 GLU ASP THR ALA ASP TYR TYR CYS ARG ALA GLN GLN LYS SEQRES 9 A 124 ILE GLY ARG ASP THR PHE ARG ASP TYR TRP GLY GLN GLY SEQRES 10 A 124 THR GLN VAL THR VAL SER SER HELIX 1 AA1 LYS A 86 THR A 90 5 5 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 21 N SER A 7 SHEET 3 AA1 4 VAL A 78 MET A 82 -1 O MET A 82 N LEU A 18 SHEET 4 AA1 4 PHE A 67 SER A 70 -1 N THR A 68 O GLN A 81 SHEET 1 AA2 6 LEU A 11 GLN A 13 0 SHEET 2 AA2 6 THR A 114 SER A 119 1 O SER A 119 N VAL A 12 SHEET 3 AA2 6 ALA A 91 ILE A 101 -1 N TYR A 93 O THR A 114 SHEET 4 AA2 6 LEU A 33 GLN A 39 -1 N LEU A 33 O GLN A 98 SHEET 5 AA2 6 ARG A 45 SER A 51 -1 O ALA A 49 N TRP A 36 SHEET 6 AA2 6 THR A 57 TYR A 59 -1 O ASN A 58 N THR A 50 SHEET 1 AA3 4 LEU A 11 GLN A 13 0 SHEET 2 AA3 4 THR A 114 SER A 119 1 O SER A 119 N VAL A 12 SHEET 3 AA3 4 ALA A 91 ILE A 101 -1 N TYR A 93 O THR A 114 SHEET 4 AA3 4 THR A 105 TRP A 110 -1 O TYR A 109 N ALA A 97 SSBOND 1 CYS A 22 CYS A 95 1555 1555 2.04 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 MODEL 1