HEADER MEMBRANE PROTEIN 17-AUG-24 9GI8 TITLE SOLUTION STRUCTURE OF HOMODIMERIC TMEM106B COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSMEMBRANE PROTEIN 106B; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: TMEM106B(54-92) IS A SYNTHETIC PEPTIDE COMPRISING COMPND 6 RESIDUES 54-92 OF TMEM106B SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS ZINC-BINDING, LYSOSOMAL, N-TERMINAL CYTOPLASMIC DOMAIN, MEMBRANE KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.SCHWEIMER,C.PEREZ-BORRAJERO,J.HENNIG REVDAT 1 26-NOV-25 9GI8 0 JRNL AUTH C.PEREZ-BORRAJERO,J.HENNIG JRNL TITL ZINC-MEDIATED REGULATION OF TMEM106B FUNCTION IN THE JRNL TITL 2 ENDOLYSOSOMAL PATHWAY REVEALED THROUGH SYSTEMATIC JRNL TITL 3 IDENTIFICATION OF TRIM2/3 UBIQUITINATION SUBSTRATES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.98.15 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9GI8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1292141020. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.6 MM NA TMEM106B(54-92), 3 MM REMARK 210 NA ZINC ION, 20 MM NA SODIUM REMARK 210 PHOSPHATE, 100 MM NA SODIUM REMARK 210 CHLORIDE, 0.5 MM NA TCEP, 90% REMARK 210 H2O/10% D2O; 1.8 MM NA REMARK 210 TMEM106B(54-92), 5 MM NA ZINC REMARK 210 ION, 20 MM NA SODIUM PHOSPHATE, REMARK 210 100 MM NA SODIUM CHLORIDE, 0.5 REMARK 210 MM NA TCEP, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D DQF-COSY; 2D 1H-1H TOCSY; 2D REMARK 210 1H-1H NOESY; 2D 1H-13C HSQC; 2D REMARK 210 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 1000 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEWJ 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 : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: DIMERIC 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 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 PRO A 62 1.63 -69.75 REMARK 500 1 ARG A 69 118.82 -163.99 REMARK 500 1 LEU A 78 170.16 -56.59 REMARK 500 1 ARG A 90 73.45 59.54 REMARK 500 1 PRO B 62 1.64 -69.75 REMARK 500 1 ARG B 69 118.72 -164.17 REMARK 500 1 LEU B 78 170.10 -56.97 REMARK 500 1 ARG B 90 73.40 59.45 REMARK 500 2 PRO A 62 1.63 -69.73 REMARK 500 2 ARG A 69 119.18 -163.78 REMARK 500 2 GLN A 77 103.60 -51.87 REMARK 500 2 PRO B 62 1.45 -69.83 REMARK 500 2 ARG B 69 118.63 -163.15 REMARK 500 2 GLN B 77 105.39 -52.00 REMARK 500 3 PRO A 62 1.48 -69.78 REMARK 500 3 ARG A 69 119.04 -162.91 REMARK 500 3 ALA A 80 47.46 -108.50 REMARK 500 3 PRO A 83 -172.08 -69.76 REMARK 500 3 SER A 85 149.25 -175.72 REMARK 500 3 ARG A 88 55.93 -111.47 REMARK 500 3 ARG A 90 69.10 -160.97 REMARK 500 3 PRO B 62 1.56 -69.76 REMARK 500 3 ARG B 69 118.32 -162.24 REMARK 500 3 ALA B 80 47.22 -108.28 REMARK 500 3 PRO B 83 -171.91 -69.73 REMARK 500 3 SER B 85 149.34 -175.67 REMARK 500 3 ARG B 88 55.91 -111.55 REMARK 500 3 ARG B 90 69.25 -161.14 REMARK 500 4 PRO A 62 1.60 -69.70 REMARK 500 4 ARG A 69 118.49 -162.79 REMARK 500 4 LEU A 78 125.49 -172.01 REMARK 500 4 ASP A 86 98.23 -69.31 REMARK 500 4 ARG A 90 73.34 52.58 REMARK 500 4 PRO B 62 1.57 -69.77 REMARK 500 4 ARG B 69 117.88 -162.42 REMARK 500 4 LEU B 78 127.56 -170.40 REMARK 500 4 ASP B 86 97.63 -68.84 REMARK 500 4 ARG B 90 73.51 52.46 REMARK 500 5 PRO A 62 1.73 -69.76 REMARK 500 5 ARG A 69 119.61 -166.65 REMARK 500 5 ARG A 72 173.89 -54.02 REMARK 500 5 GLN A 77 103.81 -53.32 REMARK 500 5 PRO A 83 -174.38 -69.82 REMARK 500 5 PRO B 62 1.74 -69.75 REMARK 500 5 ARG B 69 119.66 -166.56 REMARK 500 5 ARG B 72 173.38 -53.73 REMARK 500 5 GLN B 77 103.30 -51.98 REMARK 500 5 PRO B 83 -173.90 -69.69 REMARK 500 6 PRO A 62 1.60 -69.78 REMARK 500 6 ARG A 69 118.51 -163.08 REMARK 500 REMARK 500 THIS ENTRY HAS 182 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 61 SG REMARK 620 2 CYS A 64 SG 110.7 REMARK 620 3 CYS B 61 SG 111.2 105.5 REMARK 620 4 CYS B 64 SG 105.8 113.0 110.8 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8AMS RELATED DB: PDB REMARK 900 RELATED ID: 34953 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF HOMODIMERIC TMEM106B DBREF 9GI8 A 54 92 UNP Q9NUM4 T106B_HUMAN 54 92 DBREF 9GI8 B 54 92 UNP Q9NUM4 T106B_HUMAN 54 92 SEQRES 1 A 39 THR GLY ARG ASP SER VAL THR CYS PRO THR CYS GLN GLY SEQRES 2 A 39 THR GLY ARG ILE PRO ARG GLY GLN GLU ASN GLN LEU VAL SEQRES 3 A 39 ALA LEU ILE PRO TYR SER ASP GLN ARG LEU ARG PRO ARG SEQRES 1 B 39 THR GLY ARG ASP SER VAL THR CYS PRO THR CYS GLN GLY SEQRES 2 B 39 THR GLY ARG ILE PRO ARG GLY GLN GLU ASN GLN LEU VAL SEQRES 3 B 39 ALA LEU ILE PRO TYR SER ASP GLN ARG LEU ARG PRO ARG HET ZN A 200 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ LINK SG CYS A 61 ZN ZN A 200 1555 1555 2.34 LINK SG CYS A 64 ZN ZN A 200 1555 1555 2.34 LINK ZN ZN A 200 SG CYS B 61 1555 1555 2.34 LINK ZN ZN A 200 SG CYS B 64 1555 1555 2.33 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL CONECT 104 1213 CONECT 142 1213 CONECT 710 1213 CONECT 748 1213 CONECT 1213 104 142 710 748 MASTER 161 0 1 0 0 0 0 6 605 2 5 6 END