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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLYCOSYLATED FIVE-DOMAIN HUMAN BETA2-GLYCOPROTEIN I PURIFIED FROM BLOOD PLASMA
 
Authors :  B. Bouma, Ph. G. De Groot, J. M. H. Van Den Elsen, R. B. G. Ravelli, A. Sc M. J. A. Simmelink, R. H. W. M. Derksen, J. Kroon, P. Gros
Date :  01 Jul 99  (Deposition) - 08 Oct 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Short Consensus Repeat, Sushi, Complement Control Protein, N- Glycosylation, Multi-Domain, Membrane Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Bouma, P. G. De Groot, J. M. Van Den Elsen, R. B. Ravelli, A. Schouten, M. J. Simmelink, R. H. Derksen, J. Kroon, P. Gros
Adhesion Mechanism Of Human Beta(2)-Glycoprotein I To Phospholipids Based On Its Crystal Structure.
Embo J. V. 18 5166 1999
PubMed-ID: 10508150  |  Reference-DOI: 10.1093/EMBOJ/18.19.5166

(-) Compounds

Molecule 1 - PROTEIN (HUMAN BETA2-GLYCOPROTEIN I)
    ChainsA
    FragmentBETA2-GLYCOPROTEIN I
    OrganelleBLOOD PLASMA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1MAN1Ligand/IonALPHA-D-MANNOSE
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:143BINDING SITE FOR RESIDUE NAG A 1431
2AC2SOFTWAREASN A:164 , THR A:166 , THR A:168BINDING SITE FOR RESIDUE NAG A 1641
3AC3SOFTWAREPRO A:5 , ASN A:174 , TRP A:175 , HOH A:624 , NAG A:1742BINDING SITE FOR RESIDUE NAG A 1741
4AC4SOFTWAREASP A:8 , NAG A:1741 , MAN A:1743BINDING SITE FOR RESIDUE NAG A 1742
5AC5SOFTWARENAG A:1742BINDING SITE FOR RESIDUE MAN A 1743
6AC6SOFTWAREASN A:234 , SER A:236 , NAG A:2342BINDING SITE FOR RESIDUE NAG A 2341
7AC7SOFTWARENAG A:2341BINDING SITE FOR RESIDUE NAG A 2342

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1A:4 -A:47
2A:32 -A:60
3A:65 -A:105
4A:91 -A:118
5A:123 -A:169
6A:155 -A:181
7A:186 -A:229
8A:215 -A:241
9A:245 -A:296
10A:281 -A:306
11A:288 -A:326

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Val A:16 -Pro A:17
2Tyr A:83 -Pro A:84
3Ser A:112 -Pro A:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_008169S107NAPOH_HUMANPolymorphism1801692AS88N
2UniProtVAR_019155R154HAPOH_HUMANPolymorphism8178847AR135H
3UniProtVAR_000673V266LAPOH_HUMANPolymorphism4581AV247L
4UniProtVAR_008170C325GAPOH_HUMANPolymorphism1801689AC306G

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUSHIPS50923 Sushi/CCP/SCR domain profile.APOH_HUMAN21-81
82-139
140-202
203-262
  4A:2-62
A:63-120
A:121-183
A:184-243

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002059481ENSE00001149177chr17:64225556-64225434123APOH_HUMAN1-22221A:1-33
1.2ENST000002059482ENSE00000742667chr17:64224314-64224138177APOH_HUMAN22-81601A:3-6260
1.3ENST000002059483ENSE00000742665chr17:64222242-6422214697APOH_HUMAN81-113331A:62-9433
1.4ENST000002059484ENSE00000742663chr17:64219892-6421981677APOH_HUMAN113-139271A:94-12027
1.5ENST000002059485ENSE00000742652chr17:64216860-64216672189APOH_HUMAN139-202641A:120-18364
1.6ENST000002059486ENSE00000584156chr17:64213085-64212906180APOH_HUMAN202-262611A:183-24361
1.7ENST000002059487ENSE00000742648chr17:64210768-64210571198APOH_HUMAN262-328671A:243-30967
1.8ENST000002059488ENSE00000837173chr17:64208306-64208148159APOH_HUMAN328-345181A:309-326 (gaps)18

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:319
 aligned with APOH_HUMAN | P02749 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:326
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339      
           APOH_HUMAN    20 GRTCPKPDDLPFSTVVPLKTFYEPGEEITYSCKPGYVSRGGMRKFICPLTGLWPINTLKCTPRVCPFAGILENGAVRYTTFEYPNTISFSCNTGFYLNGADSAKCTEEGKWSPELPVCAPIICPPPSIPTFATLRVYKPSAGNNSLYRDTAVFECLPQHAMFGNDTITCTTHGNWTKLPECREVKCPFPSRPDNGFVNYPAKPTLYYKDKATFGCHDGYSLDGPEEIECTKLGNWSAMPSCKASCKVPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPC 345
               SCOP domains d1quba1 A:1-62 beta2-glycoprotein I                           d1quba2 A:63-120 beta2-glycoprotein I                     d1quba3 A:121-183 beta2-glycoprotein I                         d1quba4 A:184-243 beta2-glycoprotein I                      d1quba5 A:244-326 beta2-glycoprotein I                                              SCOP domains
               CATH domains 1qubA01 A:1-62 Complement Module, domain 1                    1qubA02 A:63-121 Complement Module, domain 1               1qubA03 A:122-183 Complement Module, domain 1                 1qubA04 A:184-243 Complement Module, domain 1               1qubA05 A:244-326 Complement Module, domain 1                                       CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1qubA01 A:186-241                                 Sushi_2-1qubA05 A:242-310                                            ---------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1qubA02 A:186-241                                 ------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1qubA03 A:186-241                                 ------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1qubA04 A:186-241                                 ------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ...ee.......eeee....ee....eeeeee...eee....eeee.............eee...........eeee........eeeeee...eeee...eeee.....ee....eeee.ee........eeeee........ee...eeeeee...eeee...eee...........eeee.ee........eeee......ee...eeeeee...eee....eee............eee.........eee....eeehhhhh........eeeeeeee....eeeeeeee...............-------.hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------N----------------------------------------------H---------------------------------------------------------------------------------------------------------------L----------------------------------------------------------G-------------------- SAPs(SNPs)
                    PROSITE -SUSHI  PDB: A:2-62 UniProt: 21-81                            SUSHI  PDB: A:63-120 UniProt: 82-139                      SUSHI  PDB: A:121-183 UniProt: 140-202                         SUSHI  PDB: A:184-243 UniProt: 203-262                      ----------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1----------------------------------------------------------Exon 1.3  PDB: A:62-94           -------------------------Exon 1.5  PDB: A:120-183 UniProt: 139-202                       -----------------------------------------------------------Exon 1.7  PDB: A:243-309 UniProt: 262-328                          ----------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: A:3-62 UniProt: 22-81                        -------------------------------Exon 1.4  PDB: A:94-120    --------------------------------------------------------------Exon 1.6  PDB: A:183-243 UniProt: 202-262                    -----------------------------------------------------------------Exon 1.8           Transcript 1 (2)
                 1qub A   1 GRTCPKPDDLPFSTVVPLKTFYEPGEEITYSCKPGYVSRGGMRKFICPLTGLWPINTLKCTPRVCPFAGILENGAVRYTTFEYPNTISFSCNTGFYLNGADSAKCTEEGKWSPELPVCAPIICPPPSIPTFATLRVYKPSAGNNSLYRDTAVFECLPQHAMFGNDTITCTTHGNWTKLPECREVKCPFPSRPDNGFVNYPAKPTLYYKDKATFGCHDGYSLDGPEEIECTKLGNWSAMPSCKASCKVPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEH-------TDASDVKPC 326
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320      
                                                                                                                                                                                                                                                                                                                                               310     318        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 5)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 5)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 5)

Asymmetric/Biological Unit
(-)
Family: Sushi (50)
1aSushi-1qubA01A:186-241
1bSushi-1qubA02A:186-241
1cSushi-1qubA03A:186-241
1dSushi-1qubA04A:186-241

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (APOH_HUMAN | P02749)
molecular function
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0060230    lipoprotein lipase activator activity    Binds to and increases the activity of a lipoprotein lipase, an enzyme that catalyzes of the hydrolysis of a lipid within a lipoprotein.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0007597    blood coagulation, intrinsic pathway    A protein activation cascade that contributes to blood coagulation and consists of the interactions among high molecular weight kininogen, prekallikrein, and factor XII that lead to the activation of clotting factor X.
    GO:0016525    negative regulation of angiogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
    GO:0030195    negative regulation of blood coagulation    Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation.
    GO:0010596    negative regulation of endothelial cell migration    Any process that decreases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    GO:0001937    negative regulation of endothelial cell proliferation    Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation.
    GO:0051918    negative regulation of fibrinolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.
    GO:0033033    negative regulation of myeloid cell apoptotic process    Any process that stops, prevents, or reduces the frequency, rate, or extent of a myeloid cell apoptotic process.
    GO:0060268    negative regulation of respiratory burst    Any process that decreases the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.
    GO:0034392    negative regulation of smooth muscle cell apoptotic process    Any process that stops, prevents, or reduces the frequency, rate, or extent of smooth muscle cell apoptotic process.
    GO:0031639    plasminogen activation    The process in which inactive plasminogen is processed to active plasmin. This process includes cleavage at an internal Arg-Val site to form an N-terminal A-chain and C-terminal B-chain held together by a disulfide bond, and can include further proteolytic cleavage events to remove the preactivation peptide.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0030194    positive regulation of blood coagulation    Any process that activates or increases the frequency, rate or extent of blood coagulation.
    GO:0051006    positive regulation of lipoprotein lipase activity    Any process that activates or increases the activity of the enzyme lipoprotein lipase.
    GO:0010898    positive regulation of triglyceride catabolic process    Any process that increases the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of triglyceride.
    GO:0030193    regulation of blood coagulation    Any process that modulates the frequency, rate or extent of blood coagulation.
    GO:0051917    regulation of fibrinolysis    Any process that modulates the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.
    GO:0034014    response to triglyceride    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a triglyceride stimulus.
    GO:0006641    triglyceride metabolic process    The chemical reactions and pathways involving triglyceride, any triester of glycerol. The three fatty acid residues may all be the same or differ in any permutation. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins.
    GO:0034197    triglyceride transport    The directed movement of triglyceride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0042627    chylomicron    A large lipoprotein particle (diameter 75-1200 nm) composed of a central core of triglycerides and cholesterol surrounded by a protein-phospholipid coating. The proteins include one molecule of apolipoprotein B-48 and may include a variety of apolipoproteins, including APOAs, APOCs and APOE. Chylomicrons are found in blood or lymph and carry lipids from the intestines into other body tissues.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0034364    high-density lipoprotein particle    A lipoprotein particle with a high density (typically 1.063-1.21 g/ml) and a diameter of 5-10 nm that contains APOAs and may contain APOCs and APOE; found in blood and carries lipids from body tissues to the liver as part of the reverse cholesterol transport process.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0031089    platelet dense granule lumen    The volume enclosed by the membrane of the platelet dense granule.
    GO:0034361    very-low-density lipoprotein particle    A triglyceride-rich lipoprotein particle that is typically composed of APOB100, APOE and APOCs and has a density of about 1.006 g/ml and a diameter of between 20-80 nm. It is found in blood and transports endogenous products (newly synthesized cholesterol and triglycerides) from the liver.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        APOH_HUMAN | P027491c1z 1g4f 1g4g 2kri 3op8 4jhs

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QUB)