HEADER CELL-SURFACE RECEPTOR 09-JAN-01 1HJ7
TITLE NMR STUDY OF A PAIR OF LDL RECEPTOR CA2+ BINDING EPIDERMAL GROWTH
TITLE 2 FACTOR-LIKE DOMAINS, 20 STRUCTURES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LDL RECEPTOR;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: CA2+ BINDING EPIDERMAL GROWTH FACTOR-LIKE DOMAIN PAIR,
COMPND 5 RESIDUES 293-372;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 CELLULAR_LOCATION: TRANSMEMBRANE;
SOURCE 6 GENE: LDLR;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE30 (QIAGEN)
KEYWDS CELL-SURFACE RECEPTOR, CALCIUM-BINDING, EGF-LIKE DOMAIN, MODULE, APO-
KEYWDS 2 E, APO-B, LDL, VLDL
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR S.SAHA,P.A.HANDFORD,I.D.CAMPBELL,A.K.DOWNING
REVDAT 5 14-FEB-18 1HJ7 1 REMARK
REVDAT 4 19-FEB-14 1HJ7 1 REMARK VERSN HETSYN
REVDAT 3 24-FEB-09 1HJ7 1 VERSN
REVDAT 2 16-AUG-01 1HJ7 1 DBREF SEQRES MASTER
REVDAT 1 11-JUL-01 1HJ7 0
JRNL AUTH S.SAHA,J.BOYD,J.M.WERNER,V.KNOTT,P.A.HANDFORD,I.D.CAMPBELL,
JRNL AUTH 2 A.K.DOWNING
JRNL TITL SOLUTION STRUCTURE OF THE LDL RECEPTOR EGF-AB PAIR: A
JRNL TITL 2 PARADIGM FOR THE ASSEMBLY OF TANDEM CALCIUM BINDING EGF
JRNL TITL 3 DOMAINS
JRNL REF STRUCTURE V. 9 451 2001
JRNL REFN ISSN 0969-2126
JRNL PMID 11435110
JRNL DOI 10.1016/S0969-2126(01)00606-2
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH J.BOYD,I.D.CAMPBELL,A.K.DOWNING
REMARK 1 TITL THE USE OF DIPOLAR COUPLINGS FOR THE STRUCTURE REFINEMENT OF
REMARK 1 TITL 2 A PAIR OF CALCIUM-BINDING EGF DOMAINS.
REMARK 1 REF METHODS MOL.BIOL. V. 173 301 2002
REMARK 1 REFN ISSN 1064-3745
REMARK 1 PMID 11859771
REMARK 1 DOI 10.1385/1-59259-184-1:301
REMARK 1 REFERENCE 2
REMARK 1 AUTH S.MALBY,R.PICKERING,S.SAHA,R.S.SMALLRIDGE,S.LINSE,
REMARK 1 AUTH 2 A.K.DOWNING
REMARK 1 TITL THE FIRST EPIDERMAL GROWTH FACTOR-LIKE DOMAIN OF THE
REMARK 1 TITL 2 LOW-DENSITY LIPOPROTEIN RECEPTOR CONTAINS A NONCANONICAL
REMARK 1 TITL 3 CALCIUM BINDING SITE
REMARK 1 REF BIOCHEMISTRY V. 40 2555 2001
REMARK 1 REFN ISSN 0006-2960
REMARK 1 PMID 11327878
REMARK 1 DOI 10.1021/BI002322L
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.851
REMARK 3 AUTHORS : BRUNGER STRUCTURAL STATISTICS: FROM EXPERIMENTAL
REMARK 3 DISTANCE CONSTRAINTS (A) RMS SIGMA DEVIATIONS FROM
REMARK 3 EXP. RESTRAINTS DEVIATIONS FROM IDEAL GEOMETRY
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN
REMARK 3 REFERENCE 1.
REMARK 4
REMARK 4 1HJ7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-JAN-01.
REMARK 100 THE DEPOSITION ID IS D_1290005541.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303
REMARK 210 PH : 6.5
REMARK 210 IONIC STRENGTH : SEE REFERENCES
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : SEE REFERENCES
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H-NOESY; COSY; TOCSY; 1H-15N
REMARK 210 HSQC; HMQC-J; HSQC-NOESY; HSQC-
REMARK 210 TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ
REMARK 210 SPECTROMETER MODEL : OMEGA
REMARK 210 SPECTROMETER MANUFACTURER : HOME-BUILT; GE
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 280
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : NO NOE, 3JHN OR 1JHN CONSTRAINTS
REMARK 210 VIOLATED BY > 0.5 A, 5 DEGREES
REMARK 210 OR 2 HERTZ
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: NOE DISTANCE CONSTRAINTS WERE DERIVED FROM CROSS PEAK
REMARK 210 INTENSITIES MEASURED IN 1H-HOMONUCLEAR AND 1H-15N HETERONUCLEAR
REMARK 210 NMR SPECTRA. COUPLING CONSTANTS USED TO DERIVE TORSION ANGLE
REMARK 210 CONSTRAINTS WERE MEASURED IN A 1H-15N HMQC-J SPECTRUM. SEE
REMARK 210 REFERENCE 1 FOR DETAILS OF 1JHN CONSTRAINT IMPLEMENTATION.
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 O ASP A 321 H PHE A 323 1.51
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 THR A 294 62.59 -160.37
REMARK 500 1 ASN A 300 -0.10 60.41
REMARK 500 1 HIS A 306 -105.38 -110.74
REMARK 500 1 LYS A 312 -72.17 -40.81
REMARK 500 1 ASP A 321 -88.23 138.81
REMARK 500 1 VAL A 326 -96.98 -97.57
REMARK 500 1 GLN A 328 19.26 40.50
REMARK 500 1 ARG A 329 -41.18 -141.92
REMARK 500 1 CYS A 331 109.80 -167.26
REMARK 500 1 ASP A 341 57.92 -150.44
REMARK 500 1 CYS A 343 -152.69 -151.24
REMARK 500 1 GLN A 345 -85.25 -132.29
REMARK 500 1 LEU A 350 -140.24 -98.17
REMARK 500 1 CYS A 358 -158.84 -142.16
REMARK 500 1 GLU A 360 105.25 -49.48
REMARK 500 1 LYS A 369 14.80 45.88
REMARK 500 2 THR A 294 39.67 -166.38
REMARK 500 2 ASN A 300 8.12 52.68
REMARK 500 2 ASN A 301 -4.10 65.14
REMARK 500 2 SER A 305 -19.78 -47.11
REMARK 500 2 HIS A 306 -117.99 -96.37
REMARK 500 2 ASP A 310 110.20 -38.17
REMARK 500 2 TYR A 315 -171.36 -51.20
REMARK 500 2 PRO A 320 -26.13 -29.29
REMARK 500 2 ASP A 321 148.88 109.38
REMARK 500 2 ALA A 327 -57.79 71.79
REMARK 500 2 GLN A 328 -2.56 132.07
REMARK 500 2 ARG A 329 29.57 -141.59
REMARK 500 2 ARG A 330 -144.55 -150.25
REMARK 500 2 CYS A 331 165.25 179.49
REMARK 500 2 ASP A 341 60.21 -150.61
REMARK 500 2 CYS A 343 -150.21 -151.05
REMARK 500 2 GLN A 345 -79.81 -140.62
REMARK 500 2 LEU A 350 -129.20 -99.30
REMARK 500 2 GLU A 351 -69.75 -120.77
REMARK 500 2 CYS A 358 -92.86 -149.19
REMARK 500 2 GLU A 359 -135.31 -85.39
REMARK 500 2 LYS A 369 3.85 56.25
REMARK 500 3 THR A 294 -134.48 -157.72
REMARK 500 3 ASN A 295 70.75 40.40
REMARK 500 3 ASN A 300 6.35 56.04
REMARK 500 3 HIS A 306 -112.90 -101.33
REMARK 500 3 LYS A 312 -86.69 -41.41
REMARK 500 3 PRO A 320 -16.22 -44.92
REMARK 500 3 ASP A 321 138.68 103.15
REMARK 500 3 ALA A 327 -49.49 -159.09
REMARK 500 3 GLN A 328 2.67 133.11
REMARK 500 3 ARG A 329 -33.62 -131.16
REMARK 500 3 ARG A 330 -144.08 -101.54
REMARK 500 3 CYS A 331 122.04 179.38
REMARK 500
REMARK 500 THIS ENTRY HAS 377 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 CA A 391 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LEU A 311 O
REMARK 620 2 GLU A 296 OE1 149.1
REMARK 620 3 ASP A 310 OD1 72.8 98.9
REMARK 620 4 ASP A 310 OD2 120.7 53.9 48.6
REMARK 620 5 THR A 294 O 156.9 46.5 89.5 46.6
REMARK 620 6 THR A 294 OG1 136.1 73.2 125.8 92.0 45.8
REMARK 620 7 GLU A 296 OE2 133.0 48.9 147.8 101.0 69.3 53.8
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 392 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 333 OD1
REMARK 620 2 ILE A 334 O 79.7
REMARK 620 3 GLU A 336 OE1 145.3 71.2
REMARK 620 4 ASN A 349 OD1 139.1 82.0 55.4
REMARK 620 5 ASP A 333 OD2 45.9 95.0 152.7 100.4
REMARK 620 6 LEU A 350 O 83.2 151.4 130.9 96.6 57.0
REMARK 620 7 GLU A 336 OE2 99.7 58.3 48.7 101.2 142.3 148.2
REMARK 620 N 1 2 3 4 5 6
REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED.
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 391
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 392
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1AJJ RELATED DB: PDB
REMARK 900 LDL RECEPTOR LIGAND-BINDING MODULE 5, CALCIUM-COORDINATING
REMARK 900 RELATED ID: 1D2J RELATED DB: PDB
REMARK 900 LDL RECEPTOR LIGAND-BINDING MODULE 6
REMARK 900 RELATED ID: 1F5Y RELATED DB: PDB
REMARK 900 NMR STRUCTURE OF A CONCATEMER OF THE FIRST AND SECOND LIGAND-
REMARK 900 BINDING MODULES OF THE HUMAN LDL RECEPTOR
REMARK 900 RELATED ID: 1F8Z RELATED DB: PDB
REMARK 900 NMR STRUCTURE OF THE SIXTH LIGAND-BINDING MODULE OF THE LDLRECEPTOR
REMARK 900 RELATED ID: 1LDL RELATED DB: PDB
REMARK 900 LOW-DENSITY LIPOPROTEIN RECEPTOR, FIRST REPEAT
REMARK 900 RELATED ID: 1LDR RELATED DB: PDB
REMARK 900 SECOND REPEAT OF THE LDL RECEPTOR LIGAND-BINDING DOMAIN
REMARK 900 RELATED ID: 1LRX RELATED DB: PDB
REMARK 900 THEORETIC MODEL OF THE HUMAN LOW-DENSITY LIPOPROTEINRECEPTOR YWTD
REMARK 900 BETA-PROPELLER DOMAIN
REMARK 900 RELATED ID: 1EMO RELATED DB: PDB
REMARK 900 NMR STUDY OF A PAIR OF FIBRILLIN CA2+ BINDING EPIDERMAL GROWTH
REMARK 900 FACTOR-LIKE DOMAINS, 22 STRUCTURES
DBREF 1HJ7 A 293 372 UNP P01130 LDLR_HUMAN 314 393
SEQRES 1 A 80 GLY THR ASN GLU CYS LEU ASP ASN ASN GLY GLY CYS SER
SEQRES 2 A 80 HIS VAL CYS ASN ASP LEU LYS ILE GLY TYR GLU CYS LEU
SEQRES 3 A 80 CYS PRO ASP GLY PHE GLN LEU VAL ALA GLN ARG ARG CYS
SEQRES 4 A 80 GLU ASP ILE ASP GLU CYS GLN ASP PRO ASP THR CYS SER
SEQRES 5 A 80 GLN LEU CYS VAL ASN LEU GLU GLY GLY TYR LYS CYS GLN
SEQRES 6 A 80 CYS GLU GLU GLY PHE GLN LEU ASP PRO HIS THR LYS ALA
SEQRES 7 A 80 CYS LYS
HET CA A 391 1
HET CA A 392 1
HETNAM CA CALCIUM ION
FORMUL 2 CA 2(CA 2+)
HELIX 1 1 ASP A 299 CYS A 304 5 6
HELIX 2 2 ASP A 335 ASP A 339 5 5
SHEET 1 S1 2 VAL A 307 ASN A 309 0
SHEET 2 S1 2 GLU A 316 LEU A 318 -1 N VAL A 307 O LEU A 318
SHEET 1 S2 2 PHE A 323 LEU A 325 0
SHEET 2 S2 2 CYS A 331 ASP A 333 -1 N GLN A 324 O GLU A 332
SHEET 1 S3 2 LEU A 346 VAL A 348 0
SHEET 2 S3 2 LYS A 355 GLN A 357 -1 N LEU A 346 O GLN A 357
SSBOND 1 CYS A 297 CYS A 308 1555 1555 2.02
SSBOND 2 CYS A 304 CYS A 317 1555 1555 2.02
SSBOND 3 CYS A 319 CYS A 331 1555 1555 2.03
SSBOND 4 CYS A 337 CYS A 347 1555 1555 2.02
SSBOND 5 CYS A 343 CYS A 356 1555 1555 2.02
SSBOND 6 CYS A 358 CYS A 371 1555 1555 2.02
LINK CA CA A 391 O LEU A 311 1555 1555 2.66
LINK CA CA A 391 OE1 GLU A 296 1555 1555 2.58
LINK CA CA A 391 OD1 ASP A 310 1555 1555 2.61
LINK CA CA A 391 OD2 ASP A 310 1555 1555 2.62
LINK CA CA A 391 O THR A 294 1555 1555 3.27
LINK CA CA A 391 OG1 THR A 294 1555 1555 2.61
LINK CA CA A 391 OE2 GLU A 296 1555 1555 2.62
LINK CA CA A 392 OD1 ASP A 333 1555 1555 2.58
LINK CA CA A 392 O ILE A 334 1555 1555 2.62
LINK CA CA A 392 OE1 GLU A 336 1555 1555 2.63
LINK CA CA A 392 OD1 ASN A 349 1555 1555 2.55
LINK CA CA A 392 OD2 ASP A 333 1555 1555 2.90
LINK CA CA A 392 O LEU A 350 1555 1555 2.64
LINK CA CA A 392 OE2 GLU A 336 1555 1555 2.59
SITE 1 AC1 4 THR A 294 GLU A 296 ASP A 310 LEU A 311
SITE 1 AC2 5 ASP A 333 ILE A 334 GLU A 336 ASN A 349
SITE 2 AC2 5 LEU A 350
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
(ATOM LINES ARE NOT SHOWN.)
END
