HEADER SIGNALING PROTEIN 16-JUN-22 8A67 TITLE BRANCHED LYS48- AND LYS63-LINKED TRI-UBIQUITIN (K48-K63-UB3) IN TITLE 2 COMPLEX WITH MATURED SYNTHETIC NANOBODY NBSL3.3Q (3RD GENERATION) COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYUBIQUITIN-B; COMPND 3 CHAIN: A, E; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: UBIQUITIN WITH C-TERMINAL TRUNCATION; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: POLYUBIQUITIN-B; COMPND 8 CHAIN: B, C, F, G; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: SYNTHETIC NANOBODY NBSL3.3Q; COMPND 13 CHAIN: D, H; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: MATURED NANOBODY NBSL3.3Q WITH N-TERMINAL PELB SIGNAL COMPND 16 SEQUENCE FOR PERIPLASMIC EXPRESSION AND C-TERMINAL 6HIS AFFINITY TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: UBB; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BRANCHED UBIQUITIN, NANOBODY, COMPLEX, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.M.LANGE,Y.KULATHU REVDAT 2 07-FEB-24 8A67 1 REMARK REVDAT 1 15-FEB-23 8A67 0 JRNL AUTH S.M.LANGE,M.R.MCFARLAND,F.LAMOLIATTE,D.KWASNA,L.SHEN, JRNL AUTH 2 I.WALLACE,I.COLE,L.A.ARMSTRONG,A.KNEBEL,C.JOHNSON, JRNL AUTH 3 V.DE CESARE,Y.KULATHU JRNL TITL COMPREHENSIVE APPROACH TO STUDY BRANCHED UBIQUITIN CHAINS JRNL TITL 2 REVEALS ROLES FOR K48-K63 BRANCHES IN VCP/P97-RELATED JRNL TITL 3 PROCESSES JRNL REF BIORXIV 2023 JRNL REFN ISSN 2692-8205 JRNL DOI 10.1101/2023.01.10.523363 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.D.ADAMS,P.V.AFONINE,G.BUNKOCZI,V.B.CHEN,I.W.DAVIS, REMARK 1 AUTH 2 N.ECHOLS,J.J.HEADD,L.W.HUNG,G.J.KAPRAL,R.W.GROSSE-KUNSTLEVE, REMARK 1 AUTH 3 A.J.MCCOY,N.W.MORIARTY,R.OEFFNER,R.J.READ,D.C.RICHARDSON, REMARK 1 AUTH 4 J.S.RICHARDSON,T.C.TERWILLIGER,P.H.ZWART REMARK 1 TITL PHENIX: A COMPREHENSIVE PYTHON-BASED SYSTEM FOR REMARK 1 TITL 2 MACROMOLECULAR STRUCTURE SOLUTION. REMARK 1 REF ACTA CRYSTALLOGR D BIOL V. 66 213 2010 REMARK 1 REF 2 CRYSTALLOGR REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 20124702 REMARK 1 DOI 10.1107/S0907444909052925 REMARK 1 REFERENCE 2 REMARK 1 AUTH C.VONRHEIN,C.FLENSBURG,P.KELLER,A.SHARFF,O.SMART,W.PACIOREK, REMARK 1 AUTH 2 T.WOMACK,G.BRICOGNE REMARK 1 TITL DATA PROCESSING AND ANALYSIS WITH THE AUTOPROC TOOLBOX. REMARK 1 REF ACTA CRYSTALLOGR D BIOL V. 67 293 2011 REMARK 1 REF 2 CRYSTALLOGR REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 21460447 REMARK 1 DOI 10.1107/S0907444911007773 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 60.8 REMARK 3 NUMBER OF REFLECTIONS : 36496 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.720 REMARK 3 FREE R VALUE TEST SET COUNT : 1721 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 52.5900 - 4.2600 0.98 4662 240 0.1658 0.2215 REMARK 3 2 4.2600 - 3.3800 0.98 4641 242 0.1443 0.1945 REMARK 3 3 3.3800 - 2.9600 0.98 4659 259 0.1819 0.2664 REMARK 3 4 2.9600 - 2.6900 0.98 4668 217 0.2058 0.2818 REMARK 3 5 2.6900 - 2.4900 0.93 4482 197 0.2220 0.2716 REMARK 3 6 2.4900 - 2.3500 0.79 3737 192 0.2295 0.2726 REMARK 3 7 2.3500 - 2.2300 0.63 3004 134 0.2229 0.2639 REMARK 3 8 2.2300 - 2.1300 0.49 2332 114 0.2171 0.2568 REMARK 3 9 2.1300 - 2.0500 0.33 1570 78 0.2152 0.2806 REMARK 3 10 2.0500 - 1.9800 0.15 730 32 0.2229 0.3013 REMARK 3 11 1.9800 - 1.9200 0.05 234 11 0.2334 0.3628 REMARK 3 12 1.9200 - 1.8600 0.01 56 5 0.2304 0.2679 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.205 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.126 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 5545 REMARK 3 ANGLE : 0.503 7489 REMARK 3 CHIRALITY : 0.043 851 REMARK 3 PLANARITY : 0.004 973 REMARK 3 DIHEDRAL : 5.214 759 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8A67 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1292123658. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87313 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36500 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 56.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.7 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 7NBB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CONCENTRATED TO 14.5 MG/ML IN REMARK 280 20 MM HEPES PH 7.5, 150 MM NACL. MIXED 200 NL PROTEIN WITH 100 REMARK 280 NL MOTHER LIQUOR (0.1 M HEPES PH 7.5, 10% 2-PROPANOL, 20% REMARK 280 PEG4000). CRYSTALS HARVESTED AND CRYO-PROTECTED WITH MOTHER REMARK 280 LIQUOR SUPPLEMENTED WITH 30% GLYCEROL., VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 6060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 350 REMARK 350 BIOMOLECULE: 2 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: 6320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -78.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, G, H 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 D -19 REMARK 465 LYS D -18 REMARK 465 TYR D -17 REMARK 465 LEU D -16 REMARK 465 LEU D -15 REMARK 465 PRO D -14 REMARK 465 THR D -13 REMARK 465 ALA D -12 REMARK 465 ALA D -11 REMARK 465 ALA D -10 REMARK 465 GLY D -9 REMARK 465 LEU D -8 REMARK 465 LEU D -7 REMARK 465 LEU D -6 REMARK 465 LEU D -5 REMARK 465 ALA D -4 REMARK 465 ALA D -3 REMARK 465 GLN D -2 REMARK 465 PRO D -1 REMARK 465 ALA D 0 REMARK 465 MET D 1 REMARK 465 ALA D 2 REMARK 465 GLN D 3 REMARK 465 MET H -19 REMARK 465 LYS H -18 REMARK 465 TYR H -17 REMARK 465 LEU H -16 REMARK 465 LEU H -15 REMARK 465 PRO H -14 REMARK 465 THR H -13 REMARK 465 ALA H -12 REMARK 465 ALA H -11 REMARK 465 ALA H -10 REMARK 465 GLY H -9 REMARK 465 LEU H -8 REMARK 465 LEU H -7 REMARK 465 LEU H -6 REMARK 465 LEU H -5 REMARK 465 ALA H -4 REMARK 465 ALA H -3 REMARK 465 GLN H -2 REMARK 465 PRO H -1 REMARK 465 ALA H 0 REMARK 465 MET H 1 REMARK 465 ALA H 2 REMARK 465 GLN H 3 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 ARG A 72 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 11 CG CD CE NZ REMARK 470 GLU B 24 CG CD OE1 OE2 REMARK 470 ARG B 74 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 11 CG CD CE NZ REMARK 470 LYS F 11 CG CD CE NZ REMARK 470 GLU F 51 CG CD OE1 OE2 REMARK 470 ARG F 74 CG CD NE CZ NH1 NH2 REMARK 470 GLU G 34 CG CD OE1 OE2 REMARK 470 VAL H 4 CG1 CG2 REMARK 470 ASN H 75 CG OD1 ND2 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 NZ LYS E 63 C GLY G 76 1.32 REMARK 500 NZ LYS A 63 C GLY C 76 1.32 REMARK 500 NZ LYS E 48 C GLY F 76 1.32 REMARK 500 NZ LYS A 48 C GLY B 76 1.33 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 D 75 -92.85 58.29 REMARK 500 GLN H 5 143.45 -171.95 REMARK 500 ASN H 75 -94.66 56.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH C 349 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH C 350 DISTANCE = 6.80 ANGSTROMS 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 D 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 IPA C 201 O2 REMARK 620 2 HIS D 124 NE2 97.4 REMARK 620 3 HIS D 126 ND1 98.3 3.1 REMARK 620 4 HIS D 128 NE2 98.8 1.4 3.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN H 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS H 124 NE2 REMARK 620 2 HIS H 126 ND1 110.1 REMARK 620 3 HIS H 128 NE2 104.1 104.8 REMARK 620 4 IPA H 201 O2 128.1 111.4 94.0 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7NBB RELATED DB: PDB REMARK 900 7NBB CONTAINS THE SAME UBIQUITIN CHAIN IN COMPLEX WITH NON-MATURED REMARK 900 NANOBODY NBSL3 REMARK 900 RELATED ID: 7NPO RELATED DB: PDB REMARK 900 7NPO CONTAINS THE SAME TRIUBIQUITIN CHAIN IN APO FORM DBREF 8A67 A 1 72 UNP J3QS39 J3QS39_HUMAN 1 72 DBREF 8A67 B 1 76 UNP J3QS39 J3QS39_HUMAN 1 76 DBREF 8A67 C 1 76 UNP J3QS39 J3QS39_HUMAN 1 76 DBREF 8A67 D -19 128 PDB 8A67 8A67 -19 128 DBREF 8A67 E 1 72 UNP J3QS39 J3QS39_HUMAN 1 72 DBREF 8A67 F 1 76 UNP J3QS39 J3QS39_HUMAN 1 76 DBREF 8A67 G 1 76 UNP J3QS39 J3QS39_HUMAN 1 76 DBREF 8A67 H -19 128 PDB 8A67 8A67 -19 128 SEQADV 8A67 ARG B 48 UNP J3QS39 LYS 48 ENGINEERED MUTATION SEQADV 8A67 ARG B 63 UNP J3QS39 LYS 63 ENGINEERED MUTATION SEQADV 8A67 ARG C 48 UNP J3QS39 LYS 48 ENGINEERED MUTATION SEQADV 8A67 ARG C 63 UNP J3QS39 LYS 63 ENGINEERED MUTATION SEQADV 8A67 ARG F 48 UNP J3QS39 LYS 48 ENGINEERED MUTATION SEQADV 8A67 ARG F 63 UNP J3QS39 LYS 63 ENGINEERED MUTATION SEQADV 8A67 ARG G 48 UNP J3QS39 LYS 48 ENGINEERED MUTATION SEQADV 8A67 ARG G 63 UNP J3QS39 LYS 63 ENGINEERED MUTATION SEQRES 1 A 72 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 72 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 72 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 72 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 72 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 72 THR LEU HIS LEU VAL LEU ARG SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY ARG GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN ARG GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY ARG GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN ARG GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 D 148 MET LYS TYR LEU LEU PRO THR ALA ALA ALA GLY LEU LEU SEQRES 2 D 148 LEU LEU ALA ALA GLN PRO ALA MET ALA GLN VAL GLN LEU SEQRES 3 D 148 GLN GLU SER GLY GLY GLY LEU VAL GLN ALA GLY GLY SER SEQRES 4 D 148 LEU ARG LEU SER CYS ALA ALA SER GLY SER ILE PHE ASP SEQRES 5 D 148 LEU GLY VAL MET GLY TRP TYR ARG GLN ALA PRO GLY LYS SEQRES 6 D 148 GLU ARG GLU GLN VAL ALA GLY ILE ASP TYR GLY GLY VAL SEQRES 7 D 148 THR ASN TYR ALA ASP SER VAL LYS GLY ARG PHE THR ILE SEQRES 8 D 148 SER ARG ASP ASN ASP THR VAL TYR LEU GLN MET ASN SER SEQRES 9 D 148 LEU LYS PRO GLU ASP THR ALA VAL TYR TYR CYS ALA ALA SEQRES 10 D 148 GLY ILE VAL GLY ASP GLU VAL GLY TRP ILE TYR TYR LEU SEQRES 11 D 148 TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SER HIS SEQRES 12 D 148 HIS HIS HIS HIS HIS SEQRES 1 E 72 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 E 72 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 E 72 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 E 72 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 E 72 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 E 72 THR LEU HIS LEU VAL LEU ARG SEQRES 1 F 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 F 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 F 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 F 76 GLN GLN ARG LEU ILE PHE ALA GLY ARG GLN LEU GLU ASP SEQRES 5 F 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN ARG GLU SER SEQRES 6 F 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 G 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 G 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 G 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 G 76 GLN GLN ARG LEU ILE PHE ALA GLY ARG GLN LEU GLU ASP SEQRES 5 G 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN ARG GLU SER SEQRES 6 G 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 H 148 MET LYS TYR LEU LEU PRO THR ALA ALA ALA GLY LEU LEU SEQRES 2 H 148 LEU LEU ALA ALA GLN PRO ALA MET ALA GLN VAL GLN LEU SEQRES 3 H 148 GLN GLU SER GLY GLY GLY LEU VAL GLN ALA GLY GLY SER SEQRES 4 H 148 LEU ARG LEU SER CYS ALA ALA SER GLY SER ILE PHE ASP SEQRES 5 H 148 LEU GLY VAL MET GLY TRP TYR ARG GLN ALA PRO GLY LYS SEQRES 6 H 148 GLU ARG GLU GLN VAL ALA GLY ILE ASP TYR GLY GLY VAL SEQRES 7 H 148 THR ASN TYR ALA ASP SER VAL LYS GLY ARG PHE THR ILE SEQRES 8 H 148 SER ARG ASP ASN ASP THR VAL TYR LEU GLN MET ASN SER SEQRES 9 H 148 LEU LYS PRO GLU ASP THR ALA VAL TYR TYR CYS ALA ALA SEQRES 10 H 148 GLY ILE VAL GLY ASP GLU VAL GLY TRP ILE TYR TYR LEU SEQRES 11 H 148 TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SER HIS SEQRES 12 H 148 HIS HIS HIS HIS HIS HET GOL B 101 6 HET IPA C 201 4 HET ZN D 201 1 HET CL E 101 1 HET NA E 102 1 HET GOL F 101 6 HET NA F 102 1 HET IPA H 201 4 HET ZN H 202 1 HETNAM GOL GLYCEROL HETNAM IPA ISOPROPYL ALCOHOL HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN IPA 2-PROPANOL FORMUL 9 GOL 2(C3 H8 O3) FORMUL 10 IPA 2(C3 H8 O) FORMUL 11 ZN 2(ZN 2+) FORMUL 12 CL CL 1- FORMUL 13 NA 2(NA 1+) FORMUL 18 HOH *523(H2 O) HELIX 1 AA1 THR A 22 GLY A 35 1 14 HELIX 2 AA2 PRO A 37 ASP A 39 5 3 HELIX 3 AA3 THR B 22 GLY B 35 1 14 HELIX 4 AA4 PRO B 37 ASP B 39 5 3 HELIX 5 AA5 LEU B 56 ASN B 60 5 5 HELIX 6 AA6 THR C 22 GLY C 35 1 14 HELIX 7 AA7 PRO C 37 ASP C 39 5 3 HELIX 8 AA8 LEU C 56 ASN C 60 5 5 HELIX 9 AA9 SER D 29 LEU D 33 5 5 HELIX 10 AB1 ASP D 63 LYS D 66 5 4 HELIX 11 AB2 LYS D 86 THR D 90 5 5 HELIX 12 AB3 THR E 22 GLY E 35 1 14 HELIX 13 AB4 PRO E 37 GLN E 41 5 5 HELIX 14 AB5 THR F 22 GLY F 35 1 14 HELIX 15 AB6 PRO F 37 ASP F 39 5 3 HELIX 16 AB7 LEU F 56 ASN F 60 5 5 HELIX 17 AB8 THR G 22 GLY G 35 1 14 HELIX 18 AB9 PRO G 37 ASP G 39 5 3 HELIX 19 AC1 LEU G 56 ASN G 60 5 5 HELIX 20 AC2 SER H 29 LEU H 33 5 5 HELIX 21 AC3 ASP H 63 LYS H 66 5 4 HELIX 22 AC4 LYS H 86 THR H 90 5 5 SHEET 1 AA1 5 THR A 12 GLU A 16 0 SHEET 2 AA1 5 GLN A 2 LYS A 6 -1 N ILE A 3 O LEU A 15 SHEET 3 AA1 5 THR A 66 LEU A 71 1 O LEU A 67 N LYS A 6 SHEET 4 AA1 5 GLN A 41 PHE A 45 -1 N ILE A 44 O HIS A 68 SHEET 5 AA1 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SHEET 1 AA2 5 ILE B 13 GLU B 16 0 SHEET 2 AA2 5 GLN B 2 LYS B 6 -1 N VAL B 5 O ILE B 13 SHEET 3 AA2 5 THR B 66 LEU B 71 1 O LEU B 67 N PHE B 4 SHEET 4 AA2 5 GLN B 41 PHE B 45 -1 N ARG B 42 O VAL B 70 SHEET 5 AA2 5 ARG B 48 GLN B 49 -1 O ARG B 48 N PHE B 45 SHEET 1 AA3 7 THR C 12 GLU C 16 0 SHEET 2 AA3 7 GLN C 2 LYS C 6 -1 N VAL C 5 O ILE C 13 SHEET 3 AA3 7 THR C 66 ARG C 74 1 O LEU C 67 N PHE C 4 SHEET 4 AA3 7 TRP D 106 TRP D 112 -1 O TYR D 109 N LEU C 71 SHEET 5 AA3 7 ALA D 91 ILE D 99 -1 N ILE D 99 O TYR D 108 SHEET 6 AA3 7 THR D 116 SER D 121 -1 O THR D 116 N TYR D 93 SHEET 7 AA3 7 GLY D 12 GLN D 15 1 N VAL D 14 O THR D 119 SHEET 1 AA4 8 ARG C 48 GLN C 49 0 SHEET 2 AA4 8 GLN C 41 PHE C 45 -1 N PHE C 45 O ARG C 48 SHEET 3 AA4 8 THR C 66 ARG C 74 -1 O HIS C 68 N ILE C 44 SHEET 4 AA4 8 TRP D 106 TRP D 112 -1 O TYR D 109 N LEU C 71 SHEET 5 AA4 8 ALA D 91 ILE D 99 -1 N ILE D 99 O TYR D 108 SHEET 6 AA4 8 VAL D 35 GLN D 41 -1 N TYR D 39 O TYR D 94 SHEET 7 AA4 8 GLU D 48 ASP D 54 -1 O ILE D 53 N MET D 36 SHEET 8 AA4 8 THR D 59 TYR D 61 -1 O ASN D 60 N GLY D 52 SHEET 1 AA5 4 LEU D 6 SER D 9 0 SHEET 2 AA5 4 LEU D 20 ALA D 26 -1 O SER D 23 N SER D 9 SHEET 3 AA5 4 THR D 77 MET D 82 -1 O MET D 82 N LEU D 20 SHEET 4 AA5 4 PHE D 69 ASP D 74 -1 N ASP D 74 O THR D 77 SHEET 1 AA6 5 THR E 12 GLU E 16 0 SHEET 2 AA6 5 GLN E 2 LYS E 6 -1 N ILE E 3 O LEU E 15 SHEET 3 AA6 5 THR E 66 VAL E 70 1 O LEU E 67 N PHE E 4 SHEET 4 AA6 5 ARG E 42 PHE E 45 -1 N ARG E 42 O VAL E 70 SHEET 5 AA6 5 LYS E 48 GLN E 49 -1 O LYS E 48 N PHE E 45 SHEET 1 AA7 5 ILE F 13 GLU F 16 0 SHEET 2 AA7 5 GLN F 2 LYS F 6 -1 N VAL F 5 O ILE F 13 SHEET 3 AA7 5 THR F 66 LEU F 71 1 O LEU F 67 N PHE F 4 SHEET 4 AA7 5 GLN F 41 PHE F 45 -1 N ARG F 42 O VAL F 70 SHEET 5 AA7 5 ARG F 48 GLN F 49 -1 O ARG F 48 N PHE F 45 SHEET 1 AA8 7 THR G 12 GLU G 16 0 SHEET 2 AA8 7 GLN G 2 LYS G 6 -1 N ILE G 3 O LEU G 15 SHEET 3 AA8 7 THR G 66 ARG G 74 1 O LEU G 67 N PHE G 4 SHEET 4 AA8 7 TRP H 106 TRP H 112 -1 O TYR H 109 N LEU G 71 SHEET 5 AA8 7 ALA H 91 ILE H 99 -1 N ILE H 99 O TYR H 108 SHEET 6 AA8 7 THR H 116 SER H 121 -1 O THR H 116 N TYR H 93 SHEET 7 AA8 7 GLY H 12 GLN H 15 1 N VAL H 14 O THR H 119 SHEET 1 AA9 8 ARG G 48 GLN G 49 0 SHEET 2 AA9 8 GLN G 41 PHE G 45 -1 N PHE G 45 O ARG G 48 SHEET 3 AA9 8 THR G 66 ARG G 74 -1 O HIS G 68 N ILE G 44 SHEET 4 AA9 8 TRP H 106 TRP H 112 -1 O TYR H 109 N LEU G 71 SHEET 5 AA9 8 ALA H 91 ILE H 99 -1 N ILE H 99 O TYR H 108 SHEET 6 AA9 8 VAL H 35 GLN H 41 -1 N TYR H 39 O TYR H 94 SHEET 7 AA9 8 GLU H 48 ASP H 54 -1 O ILE H 53 N MET H 36 SHEET 8 AA9 8 THR H 59 TYR H 61 -1 O ASN H 60 N GLY H 52 SHEET 1 AB1 4 LEU H 6 SER H 9 0 SHEET 2 AB1 4 LEU H 20 ALA H 26 -1 O SER H 23 N SER H 9 SHEET 3 AB1 4 THR H 77 MET H 82 -1 O MET H 82 N LEU H 20 SHEET 4 AB1 4 PHE H 69 ASP H 74 -1 N THR H 70 O GLN H 81 SSBOND 1 CYS D 24 CYS D 95 1555 1555 2.03 SSBOND 2 CYS H 24 CYS H 95 1555 1555 2.03 LINK O2 IPA C 201 ZN ZN D 201 1555 1554 2.61 LINK NE2 HIS D 124 ZN ZN D 201 1555 1555 2.28 LINK ND1 HIS D 126 ZN ZN D 201 1555 1555 2.29 LINK NE2 HIS D 128 ZN ZN D 201 1555 1555 2.29 LINK OE2 GLU E 18 NA NA E 102 1555 1555 2.31 LINK OE2 GLU F 34 NA NA F 102 1555 1555 2.32 LINK NE2 HIS H 124 ZN ZN H 202 1555 1555 2.29 LINK ND1 HIS H 126 ZN ZN H 202 1555 1555 2.29 LINK NE2 HIS H 128 ZN ZN H 202 1555 1555 2.29 LINK O2 IPA H 201 ZN ZN H 202 1555 1555 2.63 CRYST1 57.081 58.243 61.662 78.88 67.94 80.16 P 1 4 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 0.017519 -0.003039 -0.006739 0.00000 SCALE2 0.000000 0.017426 -0.002480 0.00000 SCALE3 0.000000 0.000000 0.017675 0.00000