HEADER SIGNALING PROTEIN 02-APR-07 2PEA
TITLE NMR BASED STRUCTURE OF THE CLOSED CONFORMATION OF LYS48-LINKED DI-
TITLE 2 UBIQUITIN USING EXPERIMENTAL GLOBAL ROTATIONAL DIFFUSION TENSOR FROM
TITLE 3 NMR RELAXATION MEASUREMENTS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: UBIQUITIN;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: UBIQUITIN;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS UBIQUITIN, LYS48-LINKED DI-UBIQUITIN, POLYUBIQUITIN, SIGNALING
KEYWDS 2 PROTEIN
EXPDTA SOLUTION NMR
AUTHOR Y.RYABOV,D.FUSHMAN
REVDAT 3 16-MAR-22 2PEA 1 REMARK
REVDAT 2 24-FEB-09 2PEA 1 VERSN
REVDAT 1 10-JUL-07 2PEA 0
JRNL AUTH Y.RYABOV,D.FUSHMAN
JRNL TITL STRUCTURAL ASSEMBLY OF MULTIDOMAIN PROTEINS AND PROTEIN
JRNL TITL 2 COMPLEXES GUIDED BY THE OVERALL ROTATIONAL DIFFUSION TENSOR.
JRNL REF J.AM.CHEM.SOC. V. 129 7894 2007
JRNL REFN ISSN 0002-7863
JRNL PMID 17550252
JRNL DOI 10.1021/JA071185D
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH Y.RYABOV,C.GERAGHTY,A.VARSHNEY,D.FUSHMAN
REMARK 1 TITL AN EFFICIENT COMPUTATIONAL METHOD FOR PREDICTING ROTATIONAL
REMARK 1 TITL 2 DIFFUSION TENSORS OF GLOBULAR PROTEINS USING AN ELLIPSOID
REMARK 1 TITL 3 REPRESENTATION.
REMARK 1 REF J.AM.CHEM.SOC. V. 128 15432 2006
REMARK 1 REFN ISSN 0002-7863
REMARK 1 PMID 17132010
REMARK 1 DOI 10.1021/JA062715T
REMARK 1 REFERENCE 2
REMARK 1 AUTH Y.RYABOV,D.FUSHMAN
REMARK 1 TITL A MODEL OF INTERDOMAIN MOBILITY IN A MULTIDOMAIN PROTEIN
REMARK 1 REF J.AM.CHEM.SOC. V. 129 3315 2007
REMARK 1 REFN ISSN 0002-7863
REMARK 1 PMID 17319663
REMARK 1 DOI 10.1021/JA067667R
REMARK 1 REFERENCE 3
REMARK 1 AUTH R.VARADAN,O.WALKER,C.PICKART,D.FUSHMAN
REMARK 1 TITL STRUCTURAL PROPERTIES OF POLYUBIQUITIN CHAINS IN SOLUTION
REMARK 1 REF J.MOL.BIOL. V. 324 637 2002
REMARK 1 REFN ISSN 0022-2836
REMARK 1 PMID 12460567
REMARK 1 DOI 10.1016/S0022-2836(02)01198-1
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : ELM, ELM
REMARK 3 AUTHORS : Y.RYABOV, D.FUSHMAN (ELM), Y.RYABOV, D.FUSHMAN
REMARK 3 (ELM)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE STRUCTURE WAS DETERMINED WITH PROGRAM ELM USING COMPLETE
REMARK 3 ROTATIONAL DIFFUSION TENSOR OF DI-UBIQUITIN AS EXPERIMENTAL
REMARK 3 RESTRAINT FOR BOTH ORIENTATION AND POSITIONING OF THE INDIVIDUAL
REMARK 3 UBIQUITIN DOMAINS WITHIN THE
REMARK 3 MOLECULE. UBIQUITIN DOMAINS WHERE ORIENTED BY A RIGID BODY
REMARK 3 ROTATION USING EXPERIMENTALLY DERIVED PRINCIPAL AXES FRAME OF
REMARK 3 THE DIFFUSION TENSOR (SEE REFERENCE 2). THE RELATIVE DOMAIN
REMARK 3 POSITIONS IN DI-UBIQUITIN WERE DETERMINED BY A RIGID BODY
REMARK 3 TRANSLATION USING ALL COMPONENTS OF THE EXPERIMENTALLY DERIVED
REMARK 3 ROTATIONAL DIFFUSION TENSOR AS RESTRAINTS.
REMARK 3 FOR EACH UBIQUITIN DOMAIN THE STRUCTURE OF THE FIRST CONFORMER
REMARK 3 OF PDB ENTRY 1D3Z WAS ASSUMED. THE DEPOSITED CONFORMATION
REMARK 3 REPRESENTS ONE OF THE TWO EXPERIMENTALLY DETECTABLE
REMARK 3 CONFORMATIONS OF DI-UBIQUITIN AT PH 6.8. THE OCCUPATION
REMARK 3 PROBABILITY OF THIS CONFORMATION IS APPROXIMATELY 90%. CHAIN A
REMARK 3 CORRESPONDS TO UBIQUITIN DOMAIN THAT HAS A FREE C-TERMINUS IN
REMARK 3 DI-UBIQUITIN. CHAIN B CORRESPONDS TO UBIQUITIN DOMAIN THAT IN
REMARK 3 DI-UBIQUITIN IS LINKED VIA AN ISOPEPTIDE BOND BETWEEN ITS C-
REMARK 3 TERMINAL GLY76 AND LYS48 OF CHAIN A. THE ISOPEPTIDE BOND WAS
REMARK 3 PRESENT IN THE DI-UBIQUITIN MOLECULE IN THIS STUDY. HOWEVER,
REMARK 3 BECAUSE THIS STRUCTURE WAS OBTAINED BY A RIGID BODY ROTATION
REMARK 3 AND TRANSLATION AND NO CONSTRAINTS REPRESENTING
REMARK 3 THE INTERDOMAIN LINKAGE WERE INCLUDED, THE ISOPEPTIDE LINKAGE
REMARK 3 IS NOT PRESENT IN THE STRUCTURE. FLEXIBLE C-TERMINI OF BOTH
REMARK 3 UBIQUTIN DOMAINS (RESIDUES 73-76)WERE EXCLUDED FROM THE NMR
REMARK 3 RATA ANALYSIS AND THEREFORE ARE NOT PRESENT IN THIS STRUCTURE.
REMARK 4
REMARK 4 2PEA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAY-07.
REMARK 100 THE DEPOSITION ID IS D_1000042281.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298.0
REMARK 210 PH : 6.8
REMARK 210 IONIC STRENGTH : 20MM
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : DI-UBIQUITIN, 90% WATER/10% D20
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N T1; 15N T2; HETERONUCLEAR
REMARK 210 NOE; HSQC; TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : NULL
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465 RES C SSSEQI
REMARK 465 LEU A 73
REMARK 465 ARG A 74
REMARK 465 GLY A 75
REMARK 465 GLY A 76
REMARK 465 LEU B 73
REMARK 465 ARG B 74
REMARK 465 GLY B 75
REMARK 465 GLY B 76
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
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 HD12 LEU A 8 HG21 ILE B 44 0.95
REMARK 500 HD11 LEU A 8 CG1 ILE B 44 1.00
REMARK 500 HA THR A 9 HE1 HIS B 68 1.04
REMARK 500 O LEU A 8 CG HIS B 68 1.06
REMARK 500 CD1 LEU A 8 HG12 ILE B 44 1.07
REMARK 500 HD13 LEU A 8 HG12 ILE B 44 1.09
REMARK 500 HH11 ARG A 42 HH12 ARG B 42 1.12
REMARK 500 HD11 LEU A 8 HG12 ILE B 44 1.13
REMARK 500 O LEU A 8 ND1 HIS B 68 1.21
REMARK 500 HH12 ARG A 42 HH22 ARG B 42 1.22
REMARK 500 HD2 HIS A 68 HD23 LEU B 8 1.22
REMARK 500 HD11 LEU A 8 CB ILE B 44 1.22
REMARK 500 HG22 VAL A 70 HG11 VAL B 70 1.23
REMARK 500 HA THR A 9 CE1 HIS B 68 1.25
REMARK 500 NH1 ARG A 42 HH22 ARG B 42 1.33
REMARK 500 HH11 ARG A 42 HH22 ARG B 42 1.33
REMARK 500 H3 MET B 1 O VAL B 17 1.51
REMARK 500 H3 MET A 1 O VAL A 17 1.51
REMARK 500 CD1 LEU A 8 HG21 ILE B 44 1.55
REMARK 500 CD2 HIS A 68 HD23 LEU B 8 1.58
REMARK 500 O LEU A 8 CD2 HIS B 68 1.73
REMARK 500 CD1 LEU A 8 CG1 ILE B 44 1.78
REMARK 500 O LEU A 8 CE1 HIS B 68 1.88
REMARK 500 NH1 ARG A 42 NH2 ARG B 42 2.04
REMARK 500 CA THR A 9 CE1 HIS B 68 2.14
REMARK 500 O LEU A 8 NE2 HIS B 68 2.16
REMARK 500 O LEU A 8 CB HIS B 68 2.17
REMARK 500 CD1 LEU A 8 CB ILE B 44 2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 ARG A 54 0.15 SIDE CHAIN
REMARK 500 ARG A 72 0.25 SIDE CHAIN
REMARK 500 ARG B 54 0.15 SIDE CHAIN
REMARK 500 ARG B 72 0.25 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1D3Z RELATED DB: PDB
REMARK 900 UBIQUITIN
REMARK 900 RELATED ID: 1AAR RELATED DB: PDB
REMARK 900 DI-UBIQUITIN
REMARK 900 RELATED ID: 2BGF RELATED DB: PDB
REMARK 900 DI-UBIQUITIN
REMARK 900 RELATED ID: 2PE9 RELATED DB: PDB
REMARK 900 DI-UBIQUITIN
DBREF 2PEA A 1 76 UNP P62988 UBIQ_HUMAN 1 76
DBREF 2PEA B 1 76 UNP P62988 UBIQ_HUMAN 1 76
SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE
SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL
SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP
SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP
SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER
SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY
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 LYS GLN LEU GLU ASP
SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER
SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY
HELIX 1 1 THR A 22 GLY A 35 1 14
HELIX 2 2 PRO A 37 ASP A 39 5 3
HELIX 3 3 LEU A 56 ASN A 60 5 5
HELIX 4 4 THR B 22 GLY B 35 1 14
HELIX 5 5 PRO B 37 ASP B 39 5 3
HELIX 6 6 LEU B 56 ASN B 60 5 5
SHEET 1 A 5 THR A 12 GLU A 16 0
SHEET 2 A 5 GLN A 2 LYS A 6 -1 N VAL A 5 O ILE A 13
SHEET 3 A 5 THR A 66 LEU A 71 1 O LEU A 67 N PHE A 4
SHEET 4 A 5 GLN A 41 PHE A 45 -1 N ILE A 44 O HIS A 68
SHEET 5 A 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45
SHEET 1 B 5 THR B 12 GLU B 16 0
SHEET 2 B 5 GLN B 2 LYS B 6 -1 N VAL B 5 O ILE B 13
SHEET 3 B 5 THR B 66 LEU B 71 1 O LEU B 67 N PHE B 4
SHEET 4 B 5 GLN B 41 PHE B 45 -1 N ILE B 44 O HIS B 68
SHEET 5 B 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45
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
(ATOM LINES ARE NOT SHOWN.)
END