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(-) Description

Title :  MAC-1 I DOMAIN CADMIUM COMPLEX
 
Authors :  E. T. Baldwin
Date :  10 Jun 98  (Deposition) - 04 Nov 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  1,2
Keywords :  Cell Adhesion, Integrin, I Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. T. Baldwin, R. W. Sarver, G. L. Bryant Jr. , K. A. Curry, M. B. Fairbanks, B. C. Finzel, R. L. Garlick, R. L. Heinrikson, N. C. Horton, L. L. Kelley, A. M. Mildner, J. B. Moon, J. E. Mott, V. T. Mutchler, C. S. Tomich, K. D. Watenpaugh, V. H. Wiley
Cation Binding To The Integrin Cd11B I Domain And Activation Model Assessment
Structure V. 6 923 1998
PubMed-ID: 9687375  |  Reference-DOI: 10.1016/S0969-2126(98)00093-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CD11B
    Cell LineBL21
    Chains1, 2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidBL21
    Expression System StrainBL21 (DE3) PLYSE
    Expression System Taxid562
    Expression System VectorPET3C
    FragmentMAC-1 ALPHA DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCELL SURFACE GLYCOPROTEIN MAC-1 ALPHA SUBUNIT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit 12

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2CD3Ligand/IonCADMIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH 1:24 , SER 1:142 , SER 1:144 , ASP 1:242 , HOH 1:907BINDING SITE FOR RESIDUE CD 1 901
2AC2SOFTWAREHOH 2:18 , SER 2:442 , SER 2:444 , ASP 2:542BINDING SITE FOR RESIDUE CD 2 702
3AC3SOFTWAREHOH 1:53 , HOH 1:54 , ASP 1:149BINDING SITE FOR RESIDUE CD 2 811
4AC4SOFTWARESER 1:133 , LYS 1:168 , ARG 1:230 , GLU 1:320BINDING SITE FOR RESIDUE ACE 1 132
5AC5SOFTWARESER 2:433 , ALA 2:533 , PHE 2:534 , GLU 2:620BINDING SITE FOR RESIDUE ACE 2 432

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BHQ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys 1:290 -Pro 1:291
2Lys 2:590 -Pro 2:591

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BHQ)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VWFAPS50234 VWFA domain profile.ITAM_HUMAN150-328
 
  21:134-312
2:434-612

(-) Exons   (5, 10)

Asymmetric/Biological Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002874971ENSE00001716458chr16:31271288-31271413126ITAM_HUMAN1-10100--
1.2ENST000002874972ENSE00001304825chr16:31273013-31273118106ITAM_HUMAN10-45360--
1.3ENST000002874973ENSE00001802514chr16:31276716-31276819104ITAM_HUMAN45-80360--
1.4ENST000002874974ENSE00001675692chr16:31277132-3127720271ITAM_HUMAN80-103240--
1.5ENST000002874975ENSE00001028855chr16:31277351-31277468118ITAM_HUMAN104-143400--
1.6ENST000002874976ENSE00001028857chr16:31282275-31282405131ITAM_HUMAN143-1864421:133-170
2:433-470
38
38
1.7ENST000002874977ENSE00001191919chr16:31283168-31283313146ITAM_HUMAN187-2354921:171-219
2:471-519
49
49
1.8ENST000002874978ENSE00001028975chr16:31284686-31284839154ITAM_HUMAN235-2865221:219-270
2:519-570
52
52
1.9ENST000002874979ENSE00001028959chr16:31286870-31287020151ITAM_HUMAN287-3375121:271-321
2:571-621
51
51
1.10ENST0000028749710ENSE00001028953chr16:31287992-3128806574ITAM_HUMAN337-3612521:321-321
2:621-621
1
1
1.11ENST0000028749711ENSE00001028971chr16:31288241-31288370130ITAM_HUMAN362-405440--
1.12ENST0000028749712ENSE00001191904chr16:31289288-31289430143ITAM_HUMAN405-452480--
1.13ENST0000028749713ENSE00001691688chr16:31308835-31308975141ITAM_HUMAN453-499470--
1.14ENST0000028749714ENSE00001709132chr16:31309066-31309275210ITAM_HUMAN500-569700--
1.15ENST0000028749715ENSE00001028860chr16:31332562-31332692131ITAM_HUMAN570-613440--
1.16ENST0000028749716ENSE00001191889chr16:31332785-31332948164ITAM_HUMAN613-668560--
1.17ENST0000028749717ENSE00001191883chr16:31335720-31335874155ITAM_HUMAN668-719520--
1.18ENST0000028749718ENSE00001028868chr16:31335972-31336103132ITAM_HUMAN720-763440--
1.19ENST0000028749719ENSE00001028854chr16:31336279-3133635274ITAM_HUMAN764-788250--
1.20ENST0000028749720ENSE00001028859chr16:31336584-31336725142ITAM_HUMAN788-835480--
1.21ENST0000028749721ENSE00001028853chr16:31336821-31336943123ITAM_HUMAN836-876410--
1.22ENST0000028749722ENSE00001242102chr16:31338177-3133825680ITAM_HUMAN877-903270--
1.23ENST0000028749723ENSE00001191849chr16:31339468-3133955184ITAM_HUMAN903-931290--
1.24ENST0000028749724ENSE00001242085chr16:31340549-3134062476ITAM_HUMAN931-956260--
1.25ENST0000028749725ENSE00001242076chr16:31341119-31341226108ITAM_HUMAN957-992360--
1.26ENST0000028749726ENSE00001191843chr16:31341402-3134148584ITAM_HUMAN993-1020280--
1.27ENST0000028749727ENSE00001191837chr16:31341629-31341742114ITAM_HUMAN1021-1058380--
1.28ENST0000028749728ENSE00001191835chr16:31341825-31341926102ITAM_HUMAN1059-1092340--
1.29ENST0000028749729ENSE00001191829chr16:31342486-31342596111ITAM_HUMAN1093-1129370--
1.30ENST0000028749730ENSE00001330465chr16:31342957-313442131257ITAM_HUMAN1130-1152230--

(-) 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 1 from PDB  Type:PROTEIN  Length:189
 aligned with ITAM_HUMAN | P11215 from UniProtKB/Swiss-Prot  Length:1152

    Alignment length:189
                                   158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328         
           ITAM_HUMAN   149 SDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFRIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVITDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVNNFEALKTIQNQLREKIFAIEG 337
               SCOP domains d1bhq1_ 1: Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha subunit)                                                                                                                            SCOP domains
               CATH domains 1bhq100 1:133-321  [code=3.40.50.410, no name defined]                                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhhhhhh......eeeeeee...eeeee.hhhhhh...hhhhhh..........hhhhhhhhhhh...hhh.......eeeeeee..............hhhhhh..eeeeeeee.hhh.....hhhhhhh....hhhheeee.....hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -VWFA  PDB: 1:134-312 UniProt: 150-328                                                                                                                                              --------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: 1:133-170 [INCOMPLETE] Exon 1.7  PDB: 1:171-219 UniProt: 187-235        -----------------------------------------------------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------Exon 1.8  PDB: 1:219-270 UniProt: 235-286           Exon 1.9  PDB: 1:271-321 UniProt: 287-337           Transcript 1 (2)
                 1bhq 1 133 SDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFRIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVITDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVNNFEALKTIQNQLREKIFAIEG 321
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312         

Chain 2 from PDB  Type:PROTEIN  Length:189
 aligned with ITAM_HUMAN | P11215 from UniProtKB/Swiss-Prot  Length:1152

    Alignment length:189
                                   158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328         
           ITAM_HUMAN   149 SDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFRIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVITDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVNNFEALKTIQNQLREKIFAIEG 337
               SCOP domains d1bhq2_ 2: Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha subunit)                                                                                                                            SCOP domains
               CATH domains 1bhq200 2:433-621  [code=3.40.50.410, no name defined]                                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........hhhhhhhhhhhhhhhh.....eeeeeee.........hhhhhh...hhhhhh..........hhhhhhhhhhh...hhh.......eeeeeee..........hhhhhhhhhhh.eeeeeeee.hhhh...hhhhhhhh....hhh.eeee...hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -VWFA  PDB: 2:434-612 UniProt: 150-328                                                                                                                                              --------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: 2:433-470 [INCOMPLETE] Exon 1.7  PDB: 2:471-519 UniProt: 187-235        -----------------------------------------------------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------Exon 1.8  PDB: 2:519-570 UniProt: 235-286           Exon 1.9  PDB: 2:571-621 UniProt: 287-337           Transcript 1 (2)
                 1bhq 2 433 SDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFRIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVITDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVNNFEALKTIQNQLREKIFAIEG 621
                                   442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612         

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BHQ)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain 1,2   (ITAM_HUMAN | P11215)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0010668    ectodermal cell differentiation    The process in which relatively unspecialized cells acquire specialized structural and/or functional features of an ectodermal cell. Differentiation includes the processes involved in commitment of a cell to a specific fate.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0007229    integrin-mediated signaling pathway    A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0034142    toll-like receptor 4 signaling pathway    Any series of molecular signals generated as a consequence of binding to toll-like receptor 4.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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: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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0008305    integrin complex    A protein complex that is composed of one alpha subunit and one beta subunit, both of which are members of the integrin superfamily of cell adhesion receptors; the complex spans the plasma membrane and binds to extracellular matrix ligands, cell-surface ligands, and soluble ligands.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ITAM_HUMAN | P112151a8x 1bho 1idn 1ido 1jlm 1m1u 1mf7 1n9z 1na5 2lke 2lkj 3q3g 3qa3 4m76 4xw2

(-) Related Entries Specified in the PDB File

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