HEADER IMMUNE SYSTEM 28-JAN-26 10ND TITLE CRYO-EM STRUCTURE OF HUMAN IL-10RA IN COMPLEX WITH VHH E07 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-10 RECEPTOR SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IL-10 RECEPTOR SUBUNIT ALPHA,IL-10R SUBUNIT ALPHA,IL-10RA, COMPND 5 CDW210A,INTERLEUKIN-10 RECEPTOR SUBUNIT 1,IL-10R SUBUNIT 1,IL-10R1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: VHH ANTIBODY E07; COMPND 9 CHAIN: B; 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: IL10RA, IL10R; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 10 ORGANISM_TAXID: 9844; SOURCE 11 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 10029 KEYWDS COMPLEX, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR H.XU REVDAT 1 21-OCT-26 10ND 0 JRNL AUTH H.XU JRNL TITL CRYO-EM STRUCTURE OF HUMAN IL-10RA IN COMPLEX WITH VHH E07 JRNL REF NATURE 2026 JRNL REFN ESSN 1476-4687 JRNL DOI 10.1038/S41586-026-11176-1 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1Y6K 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) : 2.400 REMARK 3 NUMBER OF PARTICLES : 458458 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 10ND COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-26. REMARK 100 THE DEPOSITION ID IS D_1000304238. 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 : COMPLEX OF HUMAN IL-10RA WITH REMARK 245 VHH E07 AND ANTI-VHH FAB 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 : 7.50 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 : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 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) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 165000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 A 22 REMARK 465 GLY A 23 REMARK 465 THR A 24 REMARK 465 ARG A 228 REMARK 465 GLN A 229 REMARK 465 TYR A 230 REMARK 465 PHE A 231 REMARK 465 THR A 232 REMARK 465 VAL A 233 REMARK 465 THR A 234 REMARK 465 ASN A 235 REMARK 465 GLY A 236 REMARK 465 GLY A 237 REMARK 465 GLY A 238 REMARK 465 GLY A 239 REMARK 465 SER A 240 REMARK 465 HIS A 241 REMARK 465 HIS A 242 REMARK 465 HIS A 243 REMARK 465 HIS A 244 REMARK 465 HIS A 245 REMARK 465 HIS A 246 REMARK 465 HIS A 247 REMARK 465 HIS A 248 REMARK 465 LEU B 125 REMARK 465 GLU B 126 REMARK 465 HIS B 127 REMARK 465 HIS B 128 REMARK 465 HIS B 129 REMARK 465 HIS B 130 REMARK 465 HIS B 131 REMARK 465 HIS B 132 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 GLN B 1 CG CD OE1 NE2 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 GLN A 77 51.10 -92.00 REMARK 500 ASN A 136 -130.76 53.50 REMARK 500 PHE A 180 -8.62 73.20 REMARK 500 THR A 181 64.09 -100.63 REMARK 500 VAL B 48 -60.52 -108.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-75301 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN IL-10RA IN COMPLEX WITH VHH E07 DBREF 10ND A 22 235 UNP Q13651 I10R1_HUMAN 22 235 DBREF 10ND B 1 132 PDB 10ND 10ND 1 132 SEQADV 10ND GLY A 236 UNP Q13651 EXPRESSION TAG SEQADV 10ND GLY A 237 UNP Q13651 EXPRESSION TAG SEQADV 10ND GLY A 238 UNP Q13651 EXPRESSION TAG SEQADV 10ND GLY A 239 UNP Q13651 EXPRESSION TAG SEQADV 10ND SER A 240 UNP Q13651 EXPRESSION TAG SEQADV 10ND HIS A 241 UNP Q13651 EXPRESSION TAG SEQADV 10ND HIS A 242 UNP Q13651 EXPRESSION TAG SEQADV 10ND HIS A 243 UNP Q13651 EXPRESSION TAG SEQADV 10ND HIS A 244 UNP Q13651 EXPRESSION TAG SEQADV 10ND HIS A 245 UNP Q13651 EXPRESSION TAG SEQADV 10ND HIS A 246 UNP Q13651 EXPRESSION TAG SEQADV 10ND HIS A 247 UNP Q13651 EXPRESSION TAG SEQADV 10ND HIS A 248 UNP Q13651 EXPRESSION TAG SEQRES 1 A 227 HIS GLY THR GLU LEU PRO SER PRO PRO SER VAL TRP PHE SEQRES 2 A 227 GLU ALA GLU PHE PHE HIS HIS ILE LEU HIS TRP THR PRO SEQRES 3 A 227 ILE PRO ASN GLN SER GLU SER THR CYS TYR GLU VAL ALA SEQRES 4 A 227 LEU LEU ARG TYR GLY ILE GLU SER TRP ASN SER ILE SER SEQRES 5 A 227 ASN CYS SER GLN THR LEU SER TYR ASP LEU THR ALA VAL SEQRES 6 A 227 THR LEU ASP LEU TYR HIS SER ASN GLY TYR ARG ALA ARG SEQRES 7 A 227 VAL ARG ALA VAL ASP GLY SER ARG HIS SER ASN TRP THR SEQRES 8 A 227 VAL THR ASN THR ARG PHE SER VAL ASP GLU VAL THR LEU SEQRES 9 A 227 THR VAL GLY SER VAL ASN LEU GLU ILE HIS ASN GLY PHE SEQRES 10 A 227 ILE LEU GLY LYS ILE GLN LEU PRO ARG PRO LYS MET ALA SEQRES 11 A 227 PRO ALA ASN ASP THR TYR GLU SER ILE PHE SER HIS PHE SEQRES 12 A 227 ARG GLU TYR GLU ILE ALA ILE ARG LYS VAL PRO GLY ASN SEQRES 13 A 227 PHE THR PHE THR HIS LYS LYS VAL LYS HIS GLU ASN PHE SEQRES 14 A 227 SER LEU LEU THR SER GLY GLU VAL GLY GLU PHE CYS VAL SEQRES 15 A 227 GLN VAL LYS PRO SER VAL ALA SER ARG SER ASN LYS GLY SEQRES 16 A 227 MET TRP SER LYS GLU GLU CYS ILE SER LEU THR ARG GLN SEQRES 17 A 227 TYR PHE THR VAL THR ASN GLY GLY GLY GLY SER HIS HIS SEQRES 18 A 227 HIS HIS HIS HIS HIS HIS SEQRES 1 B 132 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 132 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 132 ARG THR PHE SER ALA TYR GLY MET ALA TRP TYR ARG GLN SEQRES 4 B 132 ALA PRO GLY LYS GLU ARG GLU TRP VAL ALA ALA ILE ARG SEQRES 5 B 132 TRP ILE GLY ASP SER THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 B 132 GLY ARG PHE THR ILE SER LYS ASP ASN ALA LYS ASN THR SEQRES 7 B 132 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 B 132 ALA VAL TYR TYR CYS ALA ALA LYS THR SER VAL THR SER SEQRES 9 B 132 TYR LEU SER GLU LYS SER TYR ASN TYR TRP GLY GLN GLY SEQRES 10 B 132 THR GLN VAL THR VAL SER SER LEU GLU HIS HIS HIS HIS SEQRES 11 B 132 HIS HIS FORMUL 3 HOH *24(H2 O) HELIX 1 AA1 THR A 84 SER A 93 5 10 HELIX 2 AA2 SER A 119 VAL A 123 5 5 HELIX 3 AA3 THR A 156 PHE A 161 1 6 HELIX 4 AA4 LYS B 87 THR B 91 5 5 HELIX 5 AA5 SER B 107 LYS B 109 5 3 SHEET 1 AA1 3 VAL A 32 GLU A 37 0 SHEET 2 AA1 3 HIS A 40 TRP A 45 -1 O HIS A 44 N TRP A 33 SHEET 3 AA1 3 SER A 80 ASP A 82 -1 O TYR A 81 N LEU A 43 SHEET 1 AA2 4 TRP A 69 SER A 73 0 SHEET 2 AA2 4 THR A 55 ARG A 63 -1 N LEU A 61 O ASN A 70 SHEET 3 AA2 4 TYR A 96 ASP A 104 -1 O VAL A 103 N CYS A 56 SHEET 4 AA2 4 ARG A 107 HIS A 108 -1 O ARG A 107 N ASP A 104 SHEET 1 AA3 4 TRP A 69 SER A 73 0 SHEET 2 AA3 4 THR A 55 ARG A 63 -1 N LEU A 61 O ASN A 70 SHEET 3 AA3 4 TYR A 96 ASP A 104 -1 O VAL A 103 N CYS A 56 SHEET 4 AA3 4 THR A 112 VAL A 113 -1 O THR A 112 N VAL A 100 SHEET 1 AA4 3 SER A 129 HIS A 135 0 SHEET 2 AA4 3 PHE A 138 GLN A 144 -1 O LEU A 140 N GLU A 133 SHEET 3 AA4 3 ASN A 189 LEU A 193 -1 O PHE A 190 N GLY A 141 SHEET 1 AA5 4 LYS A 183 VAL A 185 0 SHEET 2 AA5 4 ARG A 165 LYS A 173 -1 N ILE A 169 O LYS A 183 SHEET 3 AA5 4 GLU A 200 VAL A 209 -1 O GLN A 204 N ALA A 170 SHEET 4 AA5 4 GLU A 222 SER A 225 -1 O ILE A 224 N PHE A 201 SHEET 1 AA6 4 LEU B 4 SER B 7 0 SHEET 2 AA6 4 LEU B 18 ALA B 24 -1 O SER B 21 N SER B 7 SHEET 3 AA6 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 18 SHEET 4 AA6 4 PHE B 68 ASP B 73 -1 N THR B 69 O GLN B 82 SHEET 1 AA7 6 GLY B 10 GLN B 13 0 SHEET 2 AA7 6 THR B 118 SER B 123 1 O THR B 121 N VAL B 12 SHEET 3 AA7 6 ALA B 92 LYS B 99 -1 N TYR B 94 O THR B 118 SHEET 4 AA7 6 GLY B 33 GLN B 39 -1 N TYR B 37 O TYR B 95 SHEET 5 AA7 6 GLU B 46 ARG B 52 -1 O GLU B 46 N ARG B 38 SHEET 6 AA7 6 THR B 58 TYR B 60 -1 O TYR B 59 N ALA B 50 SHEET 1 AA8 4 GLY B 10 GLN B 13 0 SHEET 2 AA8 4 THR B 118 SER B 123 1 O THR B 121 N VAL B 12 SHEET 3 AA8 4 ALA B 92 LYS B 99 -1 N TYR B 94 O THR B 118 SHEET 4 AA8 4 TYR B 111 TRP B 114 -1 O TYR B 113 N ALA B 98 SSBOND 1 CYS A 202 CYS A 223 1555 1555 2.03 SSBOND 2 CYS B 22 CYS B 96 1555 1555 2.03 CISPEP 1 VAL A 174 PRO A 175 0 1.77 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 CONECT 1439 1601 CONECT 1601 1439 CONECT 1776 2370 CONECT 2370 1776 MASTER 168 0 0 5 32 0 0 6 2607 2 4 29 END