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(-) Description

Title :  AN INTERNAL LIGAND-BOUND, METASTABLE STATE OF A LEUKOCYTE INTEGRIN, AXB2
 
Authors :  M. Sen, K. Yuki, T. A. Springer
Date :  29 Oct 13  (Deposition) - 15 Jan 14  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Complement Receptor, Ic3B, Fibrinogen, Denaturated Proteins, Heparin, Icam, N-Linked Glycosylation, Membrane, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sen, K. Yuki, T. A. Springer
An Internal Ligand-Bound, Metastable State Of A Leukocyte Integrin, Alpha X Beta 2.
J. Cell Biol. V. 203 629 2013
PubMed-ID: 24385486  |  Reference-DOI: 10.1083/JCB.201308083

(-) Compounds

Molecule 1 - INTEGRIN ALPHA-X
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK-293
    Expression System Plasmid: ET10
    Expression System Taxid: 9606
    Expression System Vector Type: STABLE CELL LINES
    Fragment: CD11C
    Gene: ITGAX, CD11C
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CD11 ANTIGEN-LIKE FAMILY MEMBER C, LEU M5, LEUKOCYTE ADHESION GLYCOPROTEIN P150,95 ALPHA CHAIN, LEUKOCYTE ADHESION RECEPTOR P150,95
 
Molecule 2 - INTEGRIN BETA-2
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK-293
    Expression System Plasmid: PEF-PURO
    Expression System Taxid: 9606
    Expression System Vector Type: STABLE CELL LINES
    Fragment: CD18
    Gene: ITGB2, CD18, MFI7
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CELL SURFACE ADHESION GLYCOPROTEINS LFA-1/CR3/P150,95 SUBUNIT BETA, COMPLEMENT RECEPTOR C3 SUBUNIT BETA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 24)

Asymmetric/Biological Unit (6, 24)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA5Ligand/IonCALCIUM ION
3CL1Ligand/IonCHLORIDE ION
4MAN3Ligand/IonALPHA-D-MANNOSE
5MG2Ligand/IonMAGNESIUM ION
6NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:929 , VAL A:931 , ASN A:1031 , NAG A:1102BINDING SITE FOR RESIDUE NAG A 1101
02AC2SOFTWARENAG A:1101BINDING SITE FOR RESIDUE NAG A 1102
03AC3SOFTWAREVAL A:69 , ASN A:70 , NAG A:1104BINDING SITE FOR RESIDUE NAG A 1103
04AC4SOFTWARENAG A:1103BINDING SITE FOR RESIDUE NAG A 1104
05AC5SOFTWAREPHE A:354 , SER A:357 , PHE A:371 , ASN A:373 , MET A:374 , SER A:375 , GLN A:376 , ASN A:378 , NAG A:1106 , HOH A:1237BINDING SITE FOR RESIDUE NAG A 1105
06AC6SOFTWAREGLU A:329 , PHE A:354 , GLN A:376 , NAG A:1105 , BMA A:1107 , MAN A:1108BINDING SITE FOR RESIDUE NAG A 1106
07AC7SOFTWAREGLU A:329 , NAG A:1106 , MAN A:1108 , MAN A:1110BINDING SITE FOR RESIDUE BMA A 1107
08AC8SOFTWARENAG A:1106 , BMA A:1107 , MAN A:1109BINDING SITE FOR RESIDUE MAN A 1108
09AC9SOFTWAREGLN A:376 , MAN A:1108BINDING SITE FOR RESIDUE MAN A 1109
10BC1SOFTWARESER A:326 , SER A:327 , GLU A:329 , BMA A:1107BINDING SITE FOR RESIDUE MAN A 1110
11BC2SOFTWARETHR A:657 , ASP A:659 , ASN A:716 , THR A:718 , TYR A:741 , NAG A:1112 , ASP B:501BINDING SITE FOR RESIDUE NAG A 1111
12BC3SOFTWARENAG A:1111BINDING SITE FOR RESIDUE NAG A 1112
13BC4SOFTWAREASP A:511 , ASN A:513 , ASP A:515 , LEU A:517 , ASP A:519 , HOH A:1219BINDING SITE FOR RESIDUE CA A 1113
14BC5SOFTWAREASP A:574 , THR A:576 , ASP A:578 , LEU A:580 , ASP A:582 , HOH A:1225BINDING SITE FOR RESIDUE CA A 1114
15BC6SOFTWAREASP A:447 , ASP A:449 , ASP A:451 , SER A:453 , ASP A:455BINDING SITE FOR RESIDUE CA A 1115
16BC7SOFTWARESER A:140 , SER A:142 , THR A:207 , LYS A:242 , CL A:1117 , HOH A:1205 , HOH A:1218BINDING SITE FOR RESIDUE MG A 1116
17BC8SOFTWARESER A:140 , SER A:142 , GLY A:205 , THR A:207 , MG A:1116BINDING SITE FOR RESIDUE CL A 1117
18BC9SOFTWAREASN B:94 , NAG B:702BINDING SITE FOR RESIDUE NAG B 701
19CC1SOFTWAREPHE B:363 , NAG B:701BINDING SITE FOR RESIDUE NAG B 702
20CC2SOFTWAREASN B:620 , ALA B:624 , NAG B:704BINDING SITE FOR RESIDUE NAG B 703
21CC3SOFTWARENAG B:703BINDING SITE FOR RESIDUE NAG B 704
22CC4SOFTWAREASP B:151 , ASN B:207 , ASP B:209 , PRO B:211 , GLU B:212BINDING SITE FOR RESIDUE CA B 705
23CC5SOFTWARESER B:116 , ASP B:242 , HOH B:809 , HOH B:810 , HOH B:834BINDING SITE FOR RESIDUE CA B 706
24CC6SOFTWAREGLU A:318 , SER B:114 , SER B:116 , GLU B:212 , ASP B:242 , HOH B:806 , HOH B:807BINDING SITE FOR RESIDUE MG B 707

(-) SS Bonds  (37, 37)

Asymmetric/Biological Unit
No.Residues
1A:89 -A:107
2A:97 -A:126
3A:476 -A:487
4A:620 -A:703
5A:636 -A:693
6A:829 -A:844
7A:920 -B:674
8A:979 -A:1013
9A:1003 -A:1008
10B:3 -B:21
11B:11 -B:425
12B:14 -B:40
13B:24 -B:51
14B:169 -B:176
15B:224 -B:264
16B:364 -B:378
17B:398 -B:423
18B:427 -B:445
19B:437 -B:448
20B:450 -B:459
21B:461 -B:492
22B:475 -B:490
23B:484 -B:495
24B:497 -B:512
25B:514 -B:537
26B:519 -B:535
27B:527 -B:540
28B:542 -B:551
29B:553 -B:576
30B:560 -B:574
31B:568 -B:579
32B:581 -B:590
33B:593 -B:596
34B:600 -B:640
35B:606 -B:625
36B:609 -B:621
37B:648 -B:673

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ser A:82 -Pro A:83
2Leu A:119 -Pro A:120
3Arg A:164 -Pro A:165
4Lys A:288 -Pro A:289
5Ile A:609 -Pro A:610
6Ser B:77 -Pro B:78
7Leu B:155 -Pro B:156
8Leu B:587 -Pro B:588

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NEN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NEN)

(-) Exons   (0, 0)

(no "Exon" information available for 4NEN)

(-) 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:1063
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.........eeee...eeeeeeeeeeee..eeeeeeee......eee.................eeee....eeeeeeeeeeeee..eeeeeeeeeee......eee...........eeeeeeee......hhhhhhhhhhhhhhhh......eeeeeeee...eeeeehhhhhhhh.hhhhhhhhh.......hhhhhhhhhhh...hhhhh.....eeeeeeee.........hhhhhhhhhhhh..eeeeee.hhhh.hhhhhhhhhhhh..hhhh.eee...hhhhhhhh........hhhhh..............eeeeeeee..eeeeee.hhhhhh..eee.......eee.....hhhhh.......eeeeee..eeeeeeee.hhhhh.eeeeeee....eeeeeeee...........eeee.........eeeee........eee.eeeee...........eee.....eeeeee...eee...........eeee..hhhhhh.eeeee.ee...ee.....eeeehhhhh.........eeeee........eeeeee..eeeeee...eeeeeeeeeee...................eeeeeeeeeeeee............eeeeeeeee.........ee......eeeeeeee..eeeeeeeeeee..........eeeeeeeeeee...........ee.......eeeee.....eeeeee......eee....eeeeeeeeee.......eeeeeeee..eeee......eeeeee.....eeeeeeee.........eeeeeeeeee........eeeeee...............eeeeeeeeeee.eeeee......eeee.......eeeeeeeeeeee.....eeeeeeeeeeeee..ee.eeeeeee........eeeeee.....hhhhhhhhh.ee.....eeeeeeeeeeee....eeeeeeeeeee.hhhhhh...eeeeeeeeeeee....eee...hhhh.eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nen A    1 FNLDTEELTAFRVDSAGFGDSVVQYANSWVVVGAPQKITAADQTGGLYQCGYSTGACEPIGLQVPPEAVNMSLGLSLASTTSPSQLLACGPTVHHECGRNMYLTGLCFLLGPTQLTQRLPVSRQECPRQEQDIVFLIDGSGSISSRNFATMMNFVRAVISQFQRPSTQFSLMQFSNKFQTHFTFEEFRRSSNPLSLLASVHQLQGFTYTATAIQNVVHRLFHASYGARRDAAKILIVITDGKKEGDSLDYKDVIPMADAAGIIRYAIGVGLAFQNRNSWKELNDIASKPSQEHIFKVEDFDALKDIQNQLKEKIFAIEGTETTSSSSFELEMAQEGFSAVFTPDGPVLGAVGSFTWSGGAFLYPPNMDPTFINMSQENVDMRDSYLGYSTELALWKGVQSLVLGAPRYQHTGKAVIFTQVSRQWRMKAEVTGTQIGSYFGASLCSVDVDSDGSTDLVLIGAPHYYEQTRGGQVSVCPLPRGWRRWWCDAVLYGEQGHPWGRFGAALTVLGDVNGDKLTDVVIGAPGEEENRGAVYLFHGVLGPSISPSHSQRIAGSQLSSRLQYFGQALSGGQDLTQDGLVDLAVGARGQVLLLRTRPVLWVGVSMQFIPAEIPRSAFECREQVVSEQTLVQSNICLYIDKRSKNLLGSRDLQSSVTLDLALDPGRLSPRATFQETKTRSLSRVRVLGLKAHCENFNLLLPSCVEDSVTPITLRLNFTLVGKPLLAFRNLRPMLAADAQRYFTASLPFEDNLGISFSFPGLKSLLVGSNLELNAEVMVWNDGEDSYGTTITFSHPAGLSYRYVALHLTCDSAPVGSQGTWSTSCRINHLIFRGGAQITFLATFDVSPKAVLGDRLLLTANVSSESNTPRTSKTTFQLELPVKYAVYTVVSSHEQFTKYLCFSESEEKESHVAMHRYQVNNLGQRDLPVSINFWVPVELNQEAVWMDVEVSHPQNPSLRCSSEKIAPPASDFLAHIQKNPVLDCSIAGCLRFRCDVPSFSVQEELDFTLKGNLSFGWVRQILQKKVSVVSVAEITFDTSVYSQLPGQEAFMRAQTTTVLEKYKP 1083
                                    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       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       760       770       780       790       800       810   ||  830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      749|                                                   814|                                                                                                                                                                                                                                                                  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       760                                                    825                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:665
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh...eee..........hhhh.eehhhhhhh.......ee....eeee......ee..eeeeee.....eeeeeee.......eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee...........hhhhhhh..............eeeeeeee.hhhhhhhhhhh...........hhhhhhhhhhhhhhhhh....eeeeeeee.......hhhhhhh...............hhhhhh....hhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhheeeee......eeeeeeee.....eeeee..eee........eeeeeeeee......eeeeeee.....eeeeeeee............eeee..eeee....................hhhhh......hhhhh.eeee..eeee.........ee.....ee.....ee..ee......eeee..eeee.............................eeee..eeee................hhhhhhhhhhhhhhhh......hhhhhh..eeee......eeeeee.....eeeeeeee......eeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nen B    1 QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPTSLAETQEDQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGYPIDLYYLMDLSYSMLDDLRNVKKLGGDLLRALNEITESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKECQPPFAFRHVLKLTDNSNQFQTEVGKQLISGNLDAPEGGLDAMMQVAACPEEIGWRKVTRLLVFATDDGFHFAGDGKLGAILTPNDGRCHLEDNLYKRSNEFDYPSVGQLAHKLAENNIQPIFAVTSRMVKTYEKLTEIIPKSAVGELSEDSSNVVQLIKNAYNKLSSRVFLDHNALPDTLKVTYDSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVLPQCECRCRLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQCERTTEGCLNPRRVECSGRGRCRCNVCECHSGYQLPLCQECPGCPSPCGKYISCAECLKFEKGPFGKNCSAACPGLQLSNNPVKGRTCKERDSEGCWVAYTLEQQDGMDRYLIYVDESRECCGG  676
                                    10        20        30        40        50        60       |74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424   ||  441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671     
                                                                                              68|                                                                                                                                                                                                                                                                                                                                                                428|                                                                                                                                                                                                                                                
                                                                                               73                                                                                                                                                                                                                                                                                                                                                                 436
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4NEN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NEN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NEN)

(-) Gene Ontology  (48, 61)

Asymmetric/Biological Unit(hide GO term definitions)

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  4nen
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  ITB2_HUMAN | P05107
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 Related Entries

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

UniProtKB/Swiss-Prot
        ITAX_HUMAN | P20702: 1n3y 2luv 3k6s 3k71 3k72 4neh 5es4
        ITB2_HUMAN | P05107: 1jx3 1l3y 1yuk 2jf1 2p26 2p28 2v7d 3k6s 3k71 3k72 4neh 5e6r 5e6s 5e6u 5e6v 5e6w 5e6x 5es4

(-) Related Entries Specified in the PDB File

2iue HOMOLOG
3k6s
3k71
3k72
4neh THE SAME PROTEIN CRYSTAL BUT DEHYDRATED