HEADER MEMBRANE PROTEIN 06-MAR-20 6Y97 TITLE STRUCTURE OF FULL-LENGTH CD20 IN COMPLEX WITH OBINUTUZUMAB FAB COMPND MOL_ID: 1; COMPND 2 MOLECULE: B-LYMPHOCYTE ANTIGEN CD20; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: B-LYMPHOCYTE SURFACE ANTIGEN B1,BP35,LEUKOCYTE SURFACE COMPND 5 ANTIGEN LEU-16,MEMBRANE-SPANNING 4-DOMAINS SUBFAMILY A MEMBER 1; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: WT CD20; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: OBINUTUZUMAB FAB HEAVY CHAIN; COMPND 10 CHAIN: H; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: OBINUTUZUMAB FAB LIGHT CHAIN; COMPND 14 CHAIN: L; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL: B-LYMPHOCYTE; SOURCE 6 GENE: MS4A1, CD20; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PCDNA3.1+; SOURCE 13 MOL_ID: 2; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 18 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 20 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: IGG1 EXPRESSION VECTOR; SOURCE 23 MOL_ID: 3; SOURCE 24 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 25 ORGANISM_COMMON: HUMAN; SOURCE 26 ORGANISM_TAXID: 9606; SOURCE 27 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 28 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 29 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 30 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 31 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 32 EXPRESSION_SYSTEM_PLASMID: PCDNA3.1 + KEYWDS CANCER IMMUNOTHERAPY, THERAPEUTIC ANTIBODY, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR A.KUMAR,N.REYES REVDAT 2 16-OCT-24 6Y97 1 REMARK REVDAT 1 26-AUG-20 6Y97 0 JRNL AUTH A.KUMAR,C.PLANCHAIS,R.FRONZES,H.MOUQUET,N.REYES JRNL TITL BINDING MECHANISMS OF THERAPEUTIC ANTIBODIES TO HUMAN CD20. JRNL REF SCIENCE V. 369 793 2020 JRNL REFN ESSN 1095-9203 JRNL PMID 32792392 JRNL DOI 10.1126/SCIENCE.ABB8008 REMARK 2 REMARK 2 RESOLUTION. 4.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, SERIALEM, GCTF, UCSF REMARK 3 CHIMERA, COOT, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, PHENIX, UCSF REMARK 3 CHIMERA, COOT, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 3PP4 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT 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) : 4.330 REMARK 3 NUMBER OF PARTICLES : 65203 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 6Y97 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292107121. 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 : FULL-LENGTH HUMAN ANTIGEN CD20 REMARK 245 IN COMPLEX WITH OBINUTUZUMAB REMARK 245 FAB; FULL-LENGTH HUMAN CD20; REMARK 245 OBINUTUZUMAB FAB REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.20 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : GRIDS WERE BLOT FOR 3.5 SEC. 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 : 10545 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) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4284.00 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, H, L 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 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 OH TYR B 161 OG SER H 30 2.15 REMARK 500 OH TYR A 86 O ALA A 126 2.18 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 SER A 144 149.89 -170.99 REMARK 500 ALA B 102 35.38 -99.83 REMARK 500 LEU L 11 74.28 51.42 REMARK 500 GLN L 55 42.45 37.25 REMARK 500 MET L 56 39.15 39.89 REMARK 500 ASP L 87 54.52 -93.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6Y90 RELATED DB: PDB REMARK 900 RELATED ID: 6Y92 RELATED DB: PDB REMARK 900 RELATED ID: EMD-10733 RELATED DB: EMDB REMARK 900 STRUCTURE OF FULL-LENGTH CD20 IN COMPLEX WITH OBINUTUZUMAB FAB DBREF 6Y97 A 45 213 UNP P11836 CD20_HUMAN 45 213 DBREF 6Y97 B 45 213 UNP P11836 CD20_HUMAN 45 213 DBREF 6Y97 H 2 117 PDB 6Y97 6Y97 2 117 DBREF 6Y97 L 1 110 PDB 6Y97 6Y97 1 110 SEQRES 1 A 169 PHE MET ARG GLU SER LYS THR LEU GLY ALA VAL GLN ILE SEQRES 2 A 169 MET ASN GLY LEU PHE HIS ILE ALA LEU GLY GLY LEU LEU SEQRES 3 A 169 MET ILE PRO ALA GLY ILE TYR ALA PRO ILE CYS VAL THR SEQRES 4 A 169 VAL TRP TYR PRO LEU TRP GLY GLY ILE MET TYR ILE ILE SEQRES 5 A 169 SER GLY SER LEU LEU ALA ALA THR GLU LYS ASN SER ARG SEQRES 6 A 169 LYS CYS LEU VAL LYS GLY LYS MET ILE MET ASN SER LEU SEQRES 7 A 169 SER LEU PHE ALA ALA ILE SER GLY MET ILE LEU SER ILE SEQRES 8 A 169 MET ASP ILE LEU ASN ILE LYS ILE SER HIS PHE LEU LYS SEQRES 9 A 169 MET GLU SER LEU ASN PHE ILE ARG ALA HIS THR PRO TYR SEQRES 10 A 169 ILE ASN ILE TYR ASN CYS GLU PRO ALA ASN PRO SER GLU SEQRES 11 A 169 LYS ASN SER PRO SER THR GLN TYR CYS TYR SER ILE GLN SEQRES 12 A 169 SER LEU PHE LEU GLY ILE LEU SER VAL MET LEU ILE PHE SEQRES 13 A 169 ALA PHE PHE GLN GLU LEU VAL ILE ALA GLY ILE VAL GLU SEQRES 1 B 169 PHE MET ARG GLU SER LYS THR LEU GLY ALA VAL GLN ILE SEQRES 2 B 169 MET ASN GLY LEU PHE HIS ILE ALA LEU GLY GLY LEU LEU SEQRES 3 B 169 MET ILE PRO ALA GLY ILE TYR ALA PRO ILE CYS VAL THR SEQRES 4 B 169 VAL TRP TYR PRO LEU TRP GLY GLY ILE MET TYR ILE ILE SEQRES 5 B 169 SER GLY SER LEU LEU ALA ALA THR GLU LYS ASN SER ARG SEQRES 6 B 169 LYS CYS LEU VAL LYS GLY LYS MET ILE MET ASN SER LEU SEQRES 7 B 169 SER LEU PHE ALA ALA ILE SER GLY MET ILE LEU SER ILE SEQRES 8 B 169 MET ASP ILE LEU ASN ILE LYS ILE SER HIS PHE LEU LYS SEQRES 9 B 169 MET GLU SER LEU ASN PHE ILE ARG ALA HIS THR PRO TYR SEQRES 10 B 169 ILE ASN ILE TYR ASN CYS GLU PRO ALA ASN PRO SER GLU SEQRES 11 B 169 LYS ASN SER PRO SER THR GLN TYR CYS TYR SER ILE GLN SEQRES 12 B 169 SER LEU PHE LEU GLY ILE LEU SER VAL MET LEU ILE PHE SEQRES 13 B 169 ALA PHE PHE GLN GLU LEU VAL ILE ALA GLY ILE VAL GLU SEQRES 1 H 116 VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS PRO SEQRES 2 H 116 GLY SER SER VAL LYS VAL SER CYS LYS ALA SER GLY TYR SEQRES 3 H 116 ALA PHE SER TYR SER TRP ILE ASN TRP VAL ARG GLN ALA SEQRES 4 H 116 PRO GLY GLN GLY LEU GLU TRP MET GLY ARG ILE PHE PRO SEQRES 5 H 116 GLY ASP GLY ASP THR ASP TYR ASN GLY LYS PHE LYS GLY SEQRES 6 H 116 ARG VAL THR ILE THR ALA ASP LYS SER THR SER THR ALA SEQRES 7 H 116 TYR MET GLU LEU SER SER LEU ARG SER GLU ASP THR ALA SEQRES 8 H 116 VAL TYR TYR CYS ALA ARG ASN VAL PHE ASP GLY TYR TRP SEQRES 9 H 116 LEU VAL TYR TRP GLY GLN GLY THR LEU VAL THR VAL SEQRES 1 L 110 ASP ILE VAL MET THR GLN THR PRO LEU SER LEU PRO VAL SEQRES 2 L 110 THR PRO GLY GLU PRO ALA SER ILE SER CYS ARG SER SER SEQRES 3 L 110 LYS SER LEU LEU HIS SER ASN GLY ILE THR TYR LEU TYR SEQRES 4 L 110 TRP TYR LEU GLN LYS PRO GLY GLN SER PRO GLN LEU LEU SEQRES 5 L 110 ILE TYR GLN MET SER ASN LEU VAL SER GLY VAL PRO ASP SEQRES 6 L 110 ARG PHE SER GLY SER GLY SER GLY THR ASP PHE THR LEU SEQRES 7 L 110 LYS ILE SER ARG VAL GLU ALA GLU ASP VAL GLY VAL TYR SEQRES 8 L 110 TYR CYS ALA GLN ASN LEU GLU LEU PRO TYR THR PHE GLY SEQRES 9 L 110 GLY GLY THR LYS VAL GLU HELIX 1 AA1 LYS A 50 LEU A 70 1 21 HELIX 2 AA2 PRO A 79 VAL A 84 1 6 HELIX 3 AA3 TRP A 85 LEU A 100 1 16 HELIX 4 AA4 ARG A 109 ILE A 143 1 35 HELIX 5 AA5 LEU A 152 ARG A 156 5 5 HELIX 6 AA6 ASN A 171 LYS A 175 5 5 HELIX 7 AA7 SER A 177 GLU A 213 1 37 HELIX 8 AA8 PHE B 45 THR B 51 5 7 HELIX 9 AA9 LEU B 52 MET B 71 1 20 HELIX 10 AB1 PRO B 79 VAL B 84 1 6 HELIX 11 AB2 TRP B 85 ALA B 102 1 18 HELIX 12 AB3 LEU B 112 ILE B 143 1 32 HELIX 13 AB4 LEU B 152 ALA B 157 1 6 HELIX 14 AB5 ASN B 171 ASN B 176 5 6 HELIX 15 AB6 SER B 177 GLU B 213 1 37 HELIX 16 AB7 ALA H 28 SER H 32 5 5 HELIX 17 AB8 ARG H 87 THR H 91 5 5 SHEET 1 AA1 4 GLN H 3 GLN H 6 0 SHEET 2 AA1 4 SER H 21 SER H 25 -1 O LYS H 23 N VAL H 5 SHEET 3 AA1 4 THR H 78 LEU H 83 -1 O ALA H 79 N CYS H 22 SHEET 4 AA1 4 VAL H 68 ASP H 73 -1 N THR H 71 O TYR H 80 SHEET 1 AA2 6 GLU H 10 VAL H 11 0 SHEET 2 AA2 6 THR H 113 THR H 116 1 O THR H 116 N GLU H 10 SHEET 3 AA2 6 VAL H 93 ARG H 98 -1 N TYR H 94 O THR H 113 SHEET 4 AA2 6 ILE H 34 GLN H 39 -1 N ASN H 35 O ALA H 97 SHEET 5 AA2 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA2 6 THR H 58 TYR H 60 -1 O ASP H 59 N ARG H 50 SHEET 1 AA3 4 MET L 4 THR L 7 0 SHEET 2 AA3 4 SER L 20 SER L 25 -1 O SER L 22 N THR L 7 SHEET 3 AA3 4 ASP L 75 LYS L 79 -1 O LEU L 78 N ILE L 21 SHEET 4 AA3 4 SER L 70 GLY L 71 -1 N SER L 70 O THR L 77 SHEET 1 AA4 5 ASN L 58 LEU L 59 0 SHEET 2 AA4 5 GLN L 50 TYR L 54 -1 N TYR L 54 O ASN L 58 SHEET 3 AA4 5 TYR L 39 LEU L 42 -1 N TRP L 40 O LEU L 52 SHEET 4 AA4 5 TYR L 91 GLN L 95 -1 O ALA L 94 N TYR L 39 SHEET 5 AA4 5 THR L 102 PHE L 103 -1 O THR L 102 N GLN L 95 SSBOND 1 CYS A 167 CYS A 183 1555 1555 2.03 SSBOND 2 CYS B 167 CYS B 183 1555 1555 2.03 SSBOND 3 CYS H 22 CYS H 96 1555 1555 2.03 SSBOND 4 CYS L 23 CYS L 93 1555 1555 2.03 CISPEP 1 THR L 7 PRO L 8 0 -2.96 CISPEP 2 LEU L 99 PRO L 100 0 -4.41 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