HEADER PROTEIN TRANSPORT 10-MAR-10 2KVB TITLE SOLUTION STRUCTURE OF CI-MPR DOMAIN 5 BOUND TO N-ACETYLGLUCOSAMINYL 6- TITLE 2 PHOSPHOMETHYLMANNOSIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CI-MPR_DOMAIN5; COMPND 5 SYNONYM: CI MAN-6-P RECEPTOR, CI-MPR, M6PR, INSULIN-LIKE GROWTH COMPND 6 FACTOR 2 RECEPTOR, INSULIN-LIKE GROWTH FACTOR II RECEPTOR, IGF-II COMPND 7 RECEPTOR, 300 KDA MANNOSE 6-PHOSPHATE RECEPTOR, MPR 300; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 GENE: IGF2R, M6P; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPICZ-ALPHA-A KEYWDS TRANSPORT, LYSOSOME, MANNOSE, RECEPTOR, SUGAR BINDING, GLYCOPROTEIN, KEYWDS 2 MEMBRANE, PHOSPHOPROTEIN, TRANSMEMBRANE, DISULFIDE BOND, PROTEIN KEYWDS 3 TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.J.OLSON,F.C.PETERSON,B.F.VOLKMAN,N.M.DAHMS REVDAT 6 20-NOV-24 2KVB 1 REMARK REVDAT 5 14-JUN-23 2KVB 1 REMARK REVDAT 4 05-FEB-20 2KVB 1 REMARK SEQADV REVDAT 3 25-DEC-13 2KVB 1 REMARK VERSN REVDAT 2 28-JUL-10 2KVB 1 JRNL REVDAT 1 07-JUL-10 2KVB 0 JRNL AUTH L.J.OLSON,F.C.PETERSON,A.CASTONGUAY,R.N.BOHNSACK,M.KUDO, JRNL AUTH 2 R.R.GOTSCHALL,W.M.CANFIELD,B.F.VOLKMAN,N.M.DAHMS JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF JRNL TITL 2 PHOSPHODIESTER-CONTAINING LYSOSOMAL ENZYMES BY THE JRNL TITL 3 CATION-INDEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR. JRNL REF PROC.NATL.ACAD.SCI.USA V. 107 12493 2010 JRNL REFN ISSN 0027-8424 JRNL PMID 20615935 JRNL DOI 10.1073/PNAS.1004232107 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.9.3 REMARK 3 AUTHORS : REMARK 3 SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 STRUCTURES ARE BASED ON A TOTAL OF 2325 NOE CONSTRAINTS (416 INTRA, REMARK 3 546 SEQUENTIAL, 271 MEDIUM, AND 1092 LONG RANGE) AND 189 PHI AND REMARK 3 PSI DIHEDRAL ANGLE CONSTRAINTS. REMARK 3 AUTHOR STATES THAT THE DATA WAS COLLECTED IN THE PRESENCE OF BOTH REMARK 3 RECEPTOR AND LIGAND N-ACETYLGLUCOSAMINYL 6-PHOSPHOMETHYLMANNOSIDE. REMARK 3 HOWEVER THE LIGAND COORDINATES WERE NOT REFINED AND THEREFORE NOT REMARK 3 DEPOSITED REMARK 4 REMARK 4 2KVB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000101617. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.25 MM [U-100% 13C; U-100% 15N] REMARK 210 CI-MPR DOMAIN5-1, 10 MM [U-2H] REMARK 210 BIS-TRIS-2, 150 MM SODIUM REMARK 210 CHLORIDE-3, 8 MM N- REMARK 210 ACETYLGLUCOSAMINYL 6- REMARK 210 PHOSPHOMETHYLMANNOSIDE-4, 95% REMARK 210 H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY (AROMATIC) 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 : TOPSPIN 2.1, NMRPIPE 2007, XEASY REMARK 210 1.3, GARANT 2.1, CYANA 2.1 REMARK 210 METHOD USED : AUTOMATED METHODS WERE USED FOR REMARK 210 BACKBONE CHEMICAL SHIFT REMARK 210 ASSIGNMENT AND ITERATIVE NOE REMARK 210 REFINEMENT. FINAL STRUCTURES REMARK 210 WERE OBTAINED BY MOLECULAR REMARK 210 DYNAMICS IN EXPLICIT SOLVENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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: MONOMERIC 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 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 HG1 THR A 587 OD2 ASP A 596 1.60 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 1 ALA A 581 153.87 72.72 REMARK 500 1 PHE A 583 77.98 69.93 REMARK 500 1 SER A 585 75.29 56.05 REMARK 500 1 CYS A 592 41.76 -72.76 REMARK 500 1 ALA A 613 175.66 70.00 REMARK 500 1 THR A 618 -160.35 -117.73 REMARK 500 1 CYS A 628 145.48 77.30 REMARK 500 1 ALA A 660 16.37 -144.23 REMARK 500 1 LYS A 661 98.69 -67.96 REMARK 500 1 TYR A 679 -89.51 -55.18 REMARK 500 1 ASN A 680 31.20 172.79 REMARK 500 1 ALA A 699 -72.09 -135.29 REMARK 500 1 GLN A 707 -75.27 -103.68 REMARK 500 1 ASP A 710 -44.22 -164.86 REMARK 500 1 SER A 712 -0.07 73.04 REMARK 500 2 ALA A 579 -45.56 -168.09 REMARK 500 2 GLU A 580 -56.33 70.73 REMARK 500 2 SER A 585 -174.56 -46.89 REMARK 500 2 ASP A 590 -167.55 -119.91 REMARK 500 2 ALA A 613 176.42 70.18 REMARK 500 2 THR A 618 -165.11 -124.16 REMARK 500 2 CYS A 628 145.97 74.10 REMARK 500 2 ALA A 635 -0.49 -146.72 REMARK 500 2 TYR A 679 -77.49 -43.75 REMARK 500 2 ASN A 680 14.84 170.44 REMARK 500 2 ARG A 684 78.50 62.67 REMARK 500 2 ALA A 699 -176.08 -177.38 REMARK 500 2 GLN A 707 -79.96 -99.78 REMARK 500 2 ASP A 710 -40.18 -158.02 REMARK 500 2 SER A 712 -0.01 71.54 REMARK 500 3 ALA A 579 80.18 174.14 REMARK 500 3 ASP A 590 -161.52 -117.80 REMARK 500 3 ASN A 591 98.04 -52.03 REMARK 500 3 ALA A 613 -178.90 63.27 REMARK 500 3 THR A 618 -168.34 -125.87 REMARK 500 3 CYS A 628 145.85 63.89 REMARK 500 3 ALA A 635 -43.46 -137.03 REMARK 500 3 TYR A 679 -92.56 20.81 REMARK 500 3 ASN A 680 21.30 171.24 REMARK 500 3 ARG A 684 86.30 57.96 REMARK 500 3 ALA A 699 -61.03 -169.45 REMARK 500 3 GLN A 707 -80.39 -88.81 REMARK 500 3 GLU A 708 124.37 -170.38 REMARK 500 3 ASP A 710 -43.82 -154.81 REMARK 500 4 GLU A 580 90.85 55.02 REMARK 500 4 LEU A 584 -83.07 -117.62 REMARK 500 4 ASP A 590 -98.31 -111.28 REMARK 500 4 ALA A 613 159.77 69.50 REMARK 500 4 THR A 618 -164.32 -120.27 REMARK 500 4 CYS A 628 146.54 75.52 REMARK 500 REMARK 500 THIS ENTRY HAS 280 RAMACHANDRAN OUTLIERS. 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 9 ARG A 687 0.07 SIDE CHAIN REMARK 500 15 ARG A 687 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KVA RELATED DB: PDB REMARK 900 RELATED ID: 16773 RELATED DB: BMRB DBREF 2KVB A 584 725 UNP P08169 MPRI_BOVIN 628 769 SEQADV 2KVB GLU A 578 UNP P08169 EXPRESSION TAG SEQADV 2KVB ALA A 579 UNP P08169 EXPRESSION TAG SEQADV 2KVB GLU A 580 UNP P08169 EXPRESSION TAG SEQADV 2KVB ALA A 581 UNP P08169 EXPRESSION TAG SEQADV 2KVB GLU A 582 UNP P08169 EXPRESSION TAG SEQADV 2KVB PHE A 583 UNP P08169 EXPRESSION TAG SEQRES 1 A 148 GLU ALA GLU ALA GLU PHE LEU SER ARG THR GLU GLY ASP SEQRES 2 A 148 ASN CYS THR VAL PHE ASP SER GLN ALA GLY PHE SER PHE SEQRES 3 A 148 ASP LEU THR PRO LEU THR LYS LYS ASP ALA TYR LYS VAL SEQRES 4 A 148 GLU THR ASP LYS TYR GLU PHE HIS ILE ASN VAL CYS GLY SEQRES 5 A 148 PRO VAL SER VAL GLY ALA CYS PRO PRO ASP SER GLY ALA SEQRES 6 A 148 CYS GLN VAL SER ARG SER ASP ARG LYS SER TRP ASN LEU SEQRES 7 A 148 GLY ARG SER ASN ALA LYS LEU SER TYR TYR ASP GLY MET SEQRES 8 A 148 ILE GLN LEU THR TYR ARG ASP GLY THR PRO TYR ASN ASN SEQRES 9 A 148 GLU LYS ARG THR PRO ARG ALA THR LEU ILE THR PHE LEU SEQRES 10 A 148 CYS ASP ARG ASP ALA GLY VAL GLY PHE PRO GLU TYR GLN SEQRES 11 A 148 GLU GLU ASP ASN SER THR TYR ASN PHE ARG TRP TYR THR SEQRES 12 A 148 SER TYR ALA CYS PRO HELIX 1 1 SER A 721 CYS A 724 5 4 SHEET 1 A 5 ARG A 586 GLU A 588 0 SHEET 2 A 5 LEU A 662 TYR A 665 -1 O TYR A 664 N THR A 587 SHEET 3 A 5 MET A 668 THR A 672 -1 O GLN A 670 N SER A 663 SHEET 4 A 5 PRO A 686 CYS A 695 -1 O PHE A 693 N ILE A 669 SHEET 5 A 5 THR A 677 PRO A 678 -1 N THR A 677 O ARG A 687 SHEET 1 B 6 ARG A 586 GLU A 588 0 SHEET 2 B 6 LEU A 662 TYR A 665 -1 O TYR A 664 N THR A 587 SHEET 3 B 6 MET A 668 THR A 672 -1 O GLN A 670 N SER A 663 SHEET 4 B 6 PRO A 686 CYS A 695 -1 O PHE A 693 N ILE A 669 SHEET 5 B 6 THR A 713 THR A 720 1 O PHE A 716 N THR A 692 SHEET 6 B 6 PHE A 703 GLU A 709 -1 N GLU A 705 O ARG A 717 SHEET 1 C 2 THR A 593 ASP A 596 0 SHEET 2 C 2 PHE A 601 ASP A 604 -1 O PHE A 603 N VAL A 594 SHEET 1 D 4 TYR A 614 GLU A 617 0 SHEET 2 D 4 TYR A 621 ILE A 625 -1 O PHE A 623 N VAL A 616 SHEET 3 D 4 ALA A 642 SER A 646 -1 O CYS A 643 N HIS A 624 SHEET 4 D 4 SER A 652 ASN A 654 -1 O TRP A 653 N GLN A 644 SSBOND 1 CYS A 592 CYS A 628 1555 1555 2.03 SSBOND 2 CYS A 636 CYS A 643 1555 1555 2.02 SSBOND 3 CYS A 695 CYS A 724 1555 1555 2.02 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