HEADER PROTEIN BINDING/ENDOCYTOSIS 18-DEC-09 2KRI
TITLE STRUCTURE OF A COMPLEX BETWEEN DOMAIN V OF BETA2-GLYCOPROTEIN I AND
TITLE 2 THE FOURTH LIGAND-BINDING MODULE FROM LDLR DETERMINED WITH HADDOCK
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BETA-2-GLYCOPROTEIN 1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: SUSHI-LIKE DOMAIN;
COMPND 5 SYNONYM: BETA-2-GLYCOPROTEIN I, BETA(2)GPI, B2GPI, APOLIPOPROTEIN H,
COMPND 6 APO-H, ACTIVATED PROTEIN C-BINDING PROTEIN, APC INHIBITOR,
COMPND 7 ANTICARDIOLIPIN COFACTOR;
COMPND 8 ENGINEERED: YES;
COMPND 9 MOL_ID: 2;
COMPND 10 MOLECULE: LOW-DENSITY LIPOPROTEIN RECEPTOR;
COMPND 11 CHAIN: B;
COMPND 12 FRAGMENT: LDL-RECEPTOR CLASS A 4 DOMAIN;
COMPND 13 SYNONYM: LDL RECEPTOR;
COMPND 14 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: APOH, B2G1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET 15;
SOURCE 9 MOL_ID: 2;
SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 11 ORGANISM_COMMON: HUMAN;
SOURCE 12 ORGANISM_TAXID: 9606;
SOURCE 13 GENE: LDLR;
SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 16 EXPRESSION_SYSTEM_VECTOR: PMM
KEYWDS ANTIPHOSPHOLIPID SYNDROME, THROMBOSIS, LDLR, RECEPTOR, DISULFIDE
KEYWDS 2 BOND, GLYCOPROTEIN, HEPARIN-BINDING, SUSHI, PROTEIN BINDING-
KEYWDS 3 ENDOCYTOSIS COMPLEX
EXPDTA SOLUTION NMR
AUTHOR N.BEGLOVA
REVDAT 2 06-NOV-19 2KRI 1 REMARK SEQADV
REVDAT 1 31-MAR-10 2KRI 0
JRNL AUTH C.J.LEE,A.DE BIASIO,N.BEGLOVA
JRNL TITL MODE OF INTERACTION BETWEEN BETA2GPI AND LIPOPROTEIN
JRNL TITL 2 RECEPTORS SUGGESTS MUTUALLY EXCLUSIVE BINDING OF BETA2GPI TO
JRNL TITL 3 THE RECEPTORS AND ANIONIC PHOSPHOLIPIDS.
JRNL REF STRUCTURE V. 18 366 2010
JRNL REFN ISSN 0969-2126
JRNL PMID 20223219
JRNL DOI 10.1016/J.STR.2009.12.013
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : GIFA 4.3, HADDOCK 2.0
REMARK 3 AUTHORS : DELSUC (GIFA), BONVIN (HADDOCK)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2KRI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-10.
REMARK 100 THE DEPOSITION ID IS D_1000101483.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 25
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N]
REMARK 210 ENTITY_2-1, 100 UM [U-100% 15N]
REMARK 210 ENTITY_2-2, 300 UM [U-100% 15N]
REMARK 210 ENTITY_2-3, 90% H2O/10% D2O; 600
REMARK 210 UM [U-100% 13C; U-100% 15N]
REMARK 210 ENTITY_1-4, 300 UM [U-100% 15N]
REMARK 210 ENTITY_1-5, 515 UM [U-100% 15N]
REMARK 210 ENTITY_1-6, 90% H2O/10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D
REMARK 210 HNCACB; 3D HN(CO)CA; 3D CBCA(CO)
REMARK 210 NH
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ
REMARK 210 SPECTROMETER MODEL : UNITY
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : GIFA 4.3, VNMR, HADDOCK 2.0,
REMARK 210 XCRVFIT 4.0.12
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 200
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST HADDOCK SCORE
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 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 GLY A 243
REMARK 465 SER A 244
REMARK 465 ALA A 327
REMARK 465 ARG B 164
REMARK 465 GLY B 165
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 HZ2 LYS A 317 OD1 ASP B 151 1.58
REMARK 500 HZ2 LYS A 284 OE2 GLU A 285 1.58
REMARK 500 OD1 ASP B 154 HG SER B 156 1.58
REMARK 500 OE2 GLU A 259 HZ3 LYS A 266 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 ARG A 260 75.24 -106.77
REMARK 500 ILE A 297 77.42 -102.78
REMARK 500 ALA A 314 -72.12 -159.47
REMARK 500 TRP A 316 33.66 -89.00
REMARK 500 SER B 137 -2.01 77.50
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 B 166 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 147 OD1
REMARK 620 2 TRP B 144 O 85.0
REMARK 620 3 ASP B 149 O 94.2 168.8
REMARK 620 N 1 2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 166
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 16639 RELATED DB: BMRB
DBREF 2KRI A 244 326 UNP P02749 APOH_HUMAN 263 345
DBREF 2KRI B 126 165 UNP P01130 LDLR_HUMAN 147 186
SEQADV 2KRI GLY A 243 UNP P02749 EXPRESSION TAG
SEQADV 2KRI LEU A 247 UNP P02749 VAL 266 CONFLICT
SEQADV 2KRI ALA A 327 UNP P02749 EXPRESSION TAG
SEQRES 1 A 85 GLY SER CYS LYS LEU PRO VAL LYS LYS ALA THR VAL VAL
SEQRES 2 A 85 TYR GLN GLY GLU ARG VAL LYS ILE GLN GLU LYS PHE LYS
SEQRES 3 A 85 ASN GLY MET LEU HIS GLY ASP LYS VAL SER PHE PHE CYS
SEQRES 4 A 85 LYS ASN LYS GLU LYS LYS CYS SER TYR THR GLU ASP ALA
SEQRES 5 A 85 GLN CYS ILE ASP GLY THR ILE GLU VAL PRO LYS CYS PHE
SEQRES 6 A 85 LYS GLU HIS SER SER LEU ALA PHE TRP LYS THR ASP ALA
SEQRES 7 A 85 SER ASP VAL LYS PRO CYS ALA
SEQRES 1 B 40 THR CYS GLY PRO ALA SER PHE GLN CYS ASN SER SER THR
SEQRES 2 B 40 CYS ILE PRO GLN LEU TRP ALA CYS ASP ASN ASP PRO ASP
SEQRES 3 B 40 CYS GLU ASP GLY SER ASP GLU TRP PRO GLN ARG CYS ARG
SEQRES 4 B 40 GLY
HET CA B 166 1
HETNAM CA CALCIUM ION
FORMUL 3 CA CA 2+
HELIX 1 1 ILE A 263 PHE A 267 1 5
HELIX 2 2 LEU B 143 ALA B 145 5 3
HELIX 3 3 GLY B 155 CYS B 163 5 9
SHEET 1 A 5 GLU A 259 LYS A 262 0
SHEET 2 A 5 THR A 253 TYR A 256 -1 N VAL A 254 O VAL A 261
SHEET 3 A 5 LYS A 276 ASN A 283 -1 O SER A 278 N VAL A 255
SHEET 4 A 5 CYS A 288 ILE A 297 -1 O CYS A 288 N ASN A 283
SHEET 5 A 5 THR A 300 ILE A 301 -1 O THR A 300 N ILE A 297
SHEET 1 B 2 SER B 131 GLN B 133 0
SHEET 2 B 2 CYS B 139 PRO B 141 -1 O ILE B 140 N PHE B 132
SSBOND 1 CYS A 245 CYS A 296 1555 1555 2.03
SSBOND 2 CYS A 281 CYS A 306 1555 1555 2.03
SSBOND 3 CYS A 288 CYS A 326 1555 1555 2.03
SSBOND 4 CYS B 127 CYS B 139 1555 1555 2.03
SSBOND 5 CYS B 134 CYS B 152 1555 1555 2.03
SSBOND 6 CYS B 146 CYS B 163 1555 1555 2.03
LINK OD1 ASP B 147 CA CA B 166 1555 1555 1.89
LINK O TRP B 144 CA CA B 166 1555 1555 2.01
LINK O ASP B 149 CA CA B 166 1555 1555 2.44
SITE 1 AC1 6 TRP B 144 ASP B 147 ASP B 149 ASP B 151
SITE 2 AC1 6 ASP B 157 GLU B 158
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
