HEADER MEMBRANE PROTEIN 27-AUG-23 8TZS TITLE STRUCTURE OF HUMAN WLS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN WNTLESS HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 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: WLS; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR X.QI,Q.HU,X.LI REVDAT 2 08-MAY-24 8TZS 1 JRNL REVDAT 1 18-OCT-23 8TZS 0 JRNL AUTH X.QI,Q.HU,N.ELGHOBASHI-MEINHARDT,T.LONG,H.CHEN,X.LI JRNL TITL MOLECULAR BASIS OF WNT BIOGENESIS, SECRETION, AND JRNL TITL 2 WNT7-SPECIFIC SIGNALING. JRNL REF CELL V. 186 5028 2023 JRNL REFN ISSN 1097-4172 JRNL PMID 37852257 JRNL DOI 10.1016/J.CELL.2023.09.021 REMARK 2 REMARK 2 RESOLUTION. 3.84 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) : 3.840 REMARK 3 NUMBER OF PARTICLES : 304150 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 8TZS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1000276990. 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 : WLS 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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) : 6000.00 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: 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 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 414 REMARK 465 PRO A 415 REMARK 465 ALA A 416 REMARK 465 MET A 417 REMARK 465 SER A 418 REMARK 465 GLU A 457 REMARK 465 GLY A 458 REMARK 465 HIS A 459 REMARK 465 TRP A 460 REMARK 465 LYS A 461 REMARK 465 TRP A 462 REMARK 465 GLY A 463 REMARK 465 GLY A 464 REMARK 465 VAL A 465 REMARK 465 THR A 466 REMARK 465 VAL A 467 REMARK 465 TYR A 499 REMARK 465 GLY A 500 REMARK 465 GLU A 501 REMARK 465 ASP A 502 REMARK 465 GLN A 503 REMARK 465 SER A 504 REMARK 465 ASN A 505 REMARK 465 GLY A 506 REMARK 465 ASP A 507 REMARK 465 LEU A 508 REMARK 465 GLY A 509 REMARK 465 VAL A 510 REMARK 465 HIS A 511 REMARK 465 SER A 512 REMARK 465 GLY A 513 REMARK 465 GLU A 514 REMARK 465 GLU A 515 REMARK 465 LEU A 516 REMARK 465 GLN A 517 REMARK 465 LEU A 518 REMARK 465 THR A 519 REMARK 465 THR A 520 REMARK 465 THR A 521 REMARK 465 ILE A 522 REMARK 465 THR A 523 REMARK 465 HIS A 524 REMARK 465 VAL A 525 REMARK 465 ASP A 526 REMARK 465 GLY A 527 REMARK 465 PRO A 528 REMARK 465 THR A 529 REMARK 465 GLU A 530 REMARK 465 ILE A 531 REMARK 465 TYR A 532 REMARK 465 LYS A 533 REMARK 465 LEU A 534 REMARK 465 THR A 535 REMARK 465 ARG A 536 REMARK 465 LYS A 537 REMARK 465 GLU A 538 REMARK 465 ALA A 539 REMARK 465 GLN A 540 REMARK 465 GLU A 541 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 OD1 ASN A 8 OG SER A 495 2.17 REMARK 500 NH1 ARG A 158 O PRO A 183 2.17 REMARK 500 O MET A 9 NH2 ARG A 431 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 162 CA - CB - SG ANGL. DEV. = 7.2 DEGREES REMARK 500 CYS A 179 CA - CB - SG ANGL. DEV. = 9.9 DEGREES REMARK 500 PRO A 263 CA - N - CD ANGL. DEV. = -15.7 DEGREES REMARK 500 PRO A 263 N - CD - CG ANGL. DEV. = -9.8 DEGREES REMARK 500 LEU A 440 CA - CB - CG ANGL. DEV. = 16.5 DEGREES 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 ASN A 69 28.02 48.96 REMARK 500 ASN A 88 -9.36 72.86 REMARK 500 PHE A 184 -60.78 -98.96 REMARK 500 HIS A 327 -159.56 -93.20 REMARK 500 GLU A 328 66.47 66.09 REMARK 500 THR A 371 70.40 58.71 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 LYS A 161 CYS A 162 -148.29 REMARK 500 CYS A 179 ASP A 180 -131.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-41768 RELATED DB: EMDB REMARK 900 STRUCTURE OF HUMAN WLS DBREF 8TZS A 1 541 UNP Q5T9L3 WLS_HUMAN 1 541 SEQRES 1 A 541 MET ALA GLY ALA ILE ILE GLU ASN MET SER THR LYS LYS SEQRES 2 A 541 LEU CYS ILE VAL GLY GLY ILE LEU LEU VAL PHE GLN ILE SEQRES 3 A 541 ILE ALA PHE LEU VAL GLY GLY LEU ILE ALA PRO GLY PRO SEQRES 4 A 541 THR THR ALA VAL SER TYR MET SER VAL LYS CYS VAL ASP SEQRES 5 A 541 ALA ARG LYS ASN HIS HIS LYS THR LYS TRP PHE VAL PRO SEQRES 6 A 541 TRP GLY PRO ASN HIS CYS ASP LYS ILE ARG ASP ILE GLU SEQRES 7 A 541 GLU ALA ILE PRO ARG GLU ILE GLU ALA ASN ASP ILE VAL SEQRES 8 A 541 PHE SER VAL HIS ILE PRO LEU PRO HIS MET GLU MET SER SEQRES 9 A 541 PRO TRP PHE GLN PHE MET LEU PHE ILE LEU GLN LEU ASP SEQRES 10 A 541 ILE ALA PHE LYS LEU ASN ASN GLN ILE ARG GLU ASN ALA SEQRES 11 A 541 GLU VAL SER MET ASP VAL SER LEU ALA TYR ARG ASP ASP SEQRES 12 A 541 ALA PHE ALA GLU TRP THR GLU MET ALA HIS GLU ARG VAL SEQRES 13 A 541 PRO ARG LYS LEU LYS CYS THR PHE THR SER PRO LYS THR SEQRES 14 A 541 PRO GLU HIS GLU GLY ARG TYR TYR GLU CYS ASP VAL LEU SEQRES 15 A 541 PRO PHE MET GLU ILE GLY SER VAL ALA HIS LYS PHE TYR SEQRES 16 A 541 LEU LEU ASN ILE ARG LEU PRO VAL ASN GLU LYS LYS LYS SEQRES 17 A 541 ILE ASN VAL GLY ILE GLY GLU ILE LYS ASP ILE ARG LEU SEQRES 18 A 541 VAL GLY ILE HIS GLN ASN GLY GLY PHE THR LYS VAL TRP SEQRES 19 A 541 PHE ALA MET LYS THR PHE LEU THR PRO SER ILE PHE ILE SEQRES 20 A 541 ILE MET VAL TRP TYR TRP ARG ARG ILE THR MET MET SER SEQRES 21 A 541 ARG PRO PRO VAL LEU LEU GLU LYS VAL ILE PHE ALA LEU SEQRES 22 A 541 GLY ILE SER MET THR PHE ILE ASN ILE PRO VAL GLU TRP SEQRES 23 A 541 PHE SER ILE GLY PHE ASP TRP THR TRP MET LEU LEU PHE SEQRES 24 A 541 GLY ASP ILE ARG GLN GLY ILE PHE TYR ALA MET LEU LEU SEQRES 25 A 541 SER PHE TRP ILE ILE PHE CYS GLY GLU HIS MET MET ASP SEQRES 26 A 541 GLN HIS GLU ARG ASN HIS ILE ALA GLY TYR TRP LYS GLN SEQRES 27 A 541 VAL GLY PRO ILE ALA VAL GLY SER PHE CYS LEU PHE ILE SEQRES 28 A 541 PHE ASP MET CYS GLU ARG GLY VAL GLN LEU THR ASN PRO SEQRES 29 A 541 PHE TYR SER ILE TRP THR THR ASP ILE GLY THR GLU LEU SEQRES 30 A 541 ALA MET ALA PHE ILE ILE VAL ALA GLY ILE CYS LEU CYS SEQRES 31 A 541 LEU TYR PHE LEU PHE LEU CYS PHE MET VAL PHE GLN VAL SEQRES 32 A 541 PHE ARG ASN ILE SER GLY LYS GLN SER SER LEU PRO ALA SEQRES 33 A 541 MET SER LYS VAL ARG ARG LEU HIS TYR GLU GLY LEU ILE SEQRES 34 A 541 PHE ARG PHE LYS PHE LEU MET LEU ILE THR LEU ALA CYS SEQRES 35 A 541 ALA ALA MET THR VAL ILE PHE PHE ILE VAL SER GLN VAL SEQRES 36 A 541 THR GLU GLY HIS TRP LYS TRP GLY GLY VAL THR VAL GLN SEQRES 37 A 541 VAL ASN SER ALA PHE PHE THR GLY ILE TYR GLY MET TRP SEQRES 38 A 541 ASN LEU TYR VAL PHE ALA LEU MET PHE LEU TYR ALA PRO SEQRES 39 A 541 SER HIS LYS ASN TYR GLY GLU ASP GLN SER ASN GLY ASP SEQRES 40 A 541 LEU GLY VAL HIS SER GLY GLU GLU LEU GLN LEU THR THR SEQRES 41 A 541 THR ILE THR HIS VAL ASP GLY PRO THR GLU ILE TYR LYS SEQRES 42 A 541 LEU THR ARG LYS GLU ALA GLN GLU HELIX 1 AA1 ALA A 4 MET A 9 1 6 HELIX 2 AA2 SER A 10 ALA A 36 1 27 HELIX 3 AA3 LYS A 121 GLN A 125 5 5 HELIX 4 AA4 THR A 169 GLU A 173 5 5 HELIX 5 AA5 ASN A 227 MET A 258 1 32 HELIX 6 AA6 VAL A 264 ILE A 282 1 19 HELIX 7 AA7 PRO A 283 GLU A 285 5 3 HELIX 8 AA8 TRP A 286 PHE A 291 1 6 HELIX 9 AA9 TRP A 295 HIS A 322 1 28 HELIX 10 AB1 HIS A 331 GLY A 334 5 4 HELIX 11 AB2 TYR A 335 GLN A 360 1 26 HELIX 12 AB3 ASP A 372 SER A 413 1 42 HELIX 13 AB4 VAL A 420 THR A 456 1 37 HELIX 14 AB5 PHE A 473 ALA A 493 1 21 SHEET 1 AA1 4 THR A 40 MET A 46 0 SHEET 2 AA1 4 GLU A 215 GLN A 226 -1 O HIS A 225 N THR A 41 SHEET 3 AA1 4 MET A 110 ALA A 119 -1 N GLN A 115 O ARG A 220 SHEET 4 AA1 4 LEU A 182 ILE A 187 -1 O LEU A 182 N LEU A 114 SHEET 1 AA2 5 VAL A 48 VAL A 51 0 SHEET 2 AA2 5 ILE A 90 HIS A 95 -1 O SER A 93 N VAL A 48 SHEET 3 AA2 5 PHE A 194 ARG A 200 -1 O ILE A 199 N PHE A 92 SHEET 4 AA2 5 MET A 134 ARG A 141 -1 N ASP A 135 O ARG A 200 SHEET 5 AA2 5 THR A 149 VAL A 156 -1 O MET A 151 N LEU A 138 SSBOND 1 CYS A 50 CYS A 71 1555 1555 2.03 SSBOND 2 CYS A 162 CYS A 179 1555 1555 2.04 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