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(-) Description

Title :  GHANAIAN HENIPAVIRUS (GH-M74A) ATTACHMENT GLYCOPROTEIN IN COMPLEX WITH HUMAN EPHRINB2
 
Authors :  B. Lee, O. Pernet, A. A. Ahmed, A. Zeltina, S. M. Beaty, T. A. Bowden
Date :  13 Mar 15  (Deposition) - 01 Apr 15  (Release) - 13 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,E
Biol. Unit 1:  B,C  (1x)
Biol. Unit 2:  A,E  (1x)
Keywords :  Viral Protein-Immune System Complex, Gh-M74A, Hendra Virus, Nipah Virus, Viral Attachment, Glycoprotein, Paramyxovirus, Ghv-G, Niv-G, Hev-G, Hnv, Hnv-G (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Lee, O. Pernet, A. A. Ahmed, A. Zeltina, S. M. Beaty, T. A. Bowden
Molecular Recognition Of Human Ephrinb2 Cell Surface Receptor By An Emergent African Henipavirus.
Proc. Natl. Acad. Sci. Usa V. 112 E2156 2015
PubMed-ID: 25825759  |  Reference-DOI: 10.1073/PNAS.1501690112

(-) Compounds

Molecule 1 - GLYCOPROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HUMAN EMBRYONIC KIDNEY 293T CRL-1573
    Expression System Common: HUMAN
    Expression System Plasmid: PHLSEC
    Expression System Taxid: 9606
    Fragment: RECEPTOR-BINDING B-PROPELLER DOMAIN, RESIDUES 199-632
    Organism Common: GHANA VIRUS
    Organism Scientific: BAT PARAMYXOVIRUS EID_HEL/GH-M74A/GHA/2009
    Organism Taxid: 1112631
    Other Details: N-ACETYLGLUCOSAMINE LINKAGES OBSERVED IN STRUCTURE. ASN207, ASN255, ASN327, AND ASN396
    Other Details - Source: SYNTHETICALLY OPTIMIZED CDNA
    Synonym: GHV-G
 
Molecule 2 - EPHRIN-B2
    Chains: C, E
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HUMAN EMBRYONIC KIDNEY 293T CRL-1573
    Expression System Common: HUMAN
    Expression System Plasmid: PHLSEC
    Expression System Taxid: 9606
    Fragment: RECEPTOR-BINDING DOMAIN, RESIDUES 27-167
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: N-ACETYLGLUCOSAMINE LINKAGES OBSERVED IN STRUCTURE. ASN39, ASN142
    Synonym: EPHRINB2, EPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 5, LER HTK LIGAND, HTK-L

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCE
Biological Unit 1 (1x):  BC 
Biological Unit 2 (1x): A  E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 33)

Asymmetric Unit (4, 33)
No.NameCountTypeFull Name
1ACT7Ligand/IonACETATE ION
2CL2Ligand/IonCHLORIDE ION
3NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO413Ligand/IonSULFATE ION
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO47Ligand/IonSULFATE ION
Biological Unit 2 (3, 17)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO46Ligand/IonSULFATE ION

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:218 , ARG A:592 , ARG A:599 , HOH A:2409BINDING SITE FOR RESIDUE SO4 A1618
02AC2SOFTWAREARG A:218 , TRP A:564 , ARG A:592 , HOH A:2411 , HOH A:2412BINDING SITE FOR RESIDUE SO4 A1619
03AC3SOFTWAREASN A:305 , GLU A:306 , ARG A:336 , LYS A:339 , ARG B:427 , ASN B:428BINDING SITE FOR RESIDUE SO4 A1620
04AC4SOFTWAREHIS A:384 , LYS A:385 , HOH A:2196 , HOH A:2202BINDING SITE FOR RESIDUE SO4 A1621
05AC5SOFTWARELYS A:393 , LYS A:394 , SER A:395 , HOH A:2222BINDING SITE FOR RESIDUE SO4 A1622
06AC6SOFTWAREARG B:218 , ARG B:592 , ARG B:599 , HOH B:2014 , HOH B:2340BINDING SITE FOR RESIDUE SO4 B1618
07AC7SOFTWAREARG A:431 , ASP A:432 , GLU B:370 , SER B:371 , HOH B:2146BINDING SITE FOR RESIDUE SO4 B1619
08AC8SOFTWAREARG B:284 , SER B:285 , HIS B:337 , ASN B:338BINDING SITE FOR RESIDUE SO4 B1620
09AC9SOFTWAREHIS B:384 , LYS B:385BINDING SITE FOR RESIDUE SO4 B1621
10BC1SOFTWAREACT A:1627 , ASN B:396 , SER B:398 , ARG B:399 , THR B:400 , ASP B:401 , ASP B:402 , NAG B:1627 , HOH B:2175 , HOH B:2191BINDING SITE FOR RESIDUE SO4 B1622
11BC2SOFTWAREASN A:235 , ARG A:237 , SER A:250 , TYR A:252 , LYS A:261 , GLU A:264 , HIS A:296 , SER A:297 , HOH A:2039 , HOH A:2087 , HOH A:2173BINDING SITE FOR RESIDUE SO4 A1623
12BC3SOFTWARELYS C:95 , LYS C:96 , GLN C:151 , HOH C:2056BINDING SITE FOR RESIDUE SO4 C1172
13BC4SOFTWAREASN B:235 , ARG B:237 , SER B:250 , TYR B:252 , LYS B:261 , GLU B:264 , HIS B:296 , SER B:297 , HOH B:2023 , HOH B:2034 , HOH B:2073BINDING SITE FOR RESIDUE SO4 B1623
14BC5SOFTWARELYS B:537 , SER B:538 , GLU B:539 , HOH B:2269 , HOH B:2343BINDING SITE FOR RESIDUE ACT B1624
15BC6SOFTWAREARG A:284 , SER A:285 , HIS A:337 , HOH A:2072BINDING SITE FOR RESIDUE ACT A1624
16BC7SOFTWAREPHE A:505 , LYS A:537 , SER A:538 , GLU A:539 , HOH A:2415BINDING SITE FOR RESIDUE ACT A1625
17BC8SOFTWAREPRO A:212 , THR A:213 , ILE A:214 , PHE A:559BINDING SITE FOR RESIDUE ACT A1626
18BC9SOFTWAREPRO A:493 , TYR A:494 , GLN A:554 , ILE A:555 , HOH A:2376 , ASN B:396 , SO4 B:1622 , NAG B:1627 , HOH B:2180BINDING SITE FOR RESIDUE ACT A1627
19CC1SOFTWARESER A:501 , HOH A:2363 , HOH A:2365 , ASP E:110 , ILE E:111 , LYS E:112BINDING SITE FOR RESIDUE ACT E1173
20CC2SOFTWARETYR B:295 , CYS B:311 , HIS B:331 , VAL B:333 , ILE B:343 , HOH B:2072 , GLU E:34BINDING SITE FOR RESIDUE ACT B1625
21CC3SOFTWAREARG B:381 , SER B:414 , PRO B:415 , GLN B:416 , HIS B:417BINDING SITE FOR RESIDUE CL B1626
22CC4SOFTWAREARG A:381 , SER A:414 , PRO A:415 , GLN A:416 , HIS A:417BINDING SITE FOR RESIDUE CL A1628
23CC5SOFTWAREASN A:207 , SER A:209BINDING SITE FOR MONO-SACCHARIDE NAG A1632 BOUND TO ASN A 207
24CC6SOFTWAREASN A:255 , HOH A:2041 , LYS E:133BINDING SITE FOR MONO-SACCHARIDE NAG A1629 BOUND TO ASN A 255
25CC7SOFTWARETHR A:315 , SER A:316 , LYS A:322 , ASN A:324 , ASN A:327BINDING SITE FOR MONO-SACCHARIDE NAG A1630 BOUND TO ASN A 327
26CC8SOFTWAREASN A:396 , CYS A:397 , SER A:398 , ARG A:399 , HOH A:2416 , HOH A:2417 , GLU B:478 , ASP B:488 , LEU B:490 , ARG B:552BINDING SITE FOR MONO-SACCHARIDE NAG A1631 BOUND TO ASN A 396
27CC9SOFTWAREASN B:207 , SER B:209 , GLN E:75BINDING SITE FOR MONO-SACCHARIDE NAG B1630 BOUND TO ASN B 207
28DC1SOFTWAREASN B:255 , HOH B:2344 , LYS C:133BINDING SITE FOR MONO-SACCHARIDE NAG B1629 BOUND TO ASN B 255
29DC2SOFTWARETHR B:315 , SER B:316 , LYS B:322 , ASN B:324 , ASN B:327BINDING SITE FOR MONO-SACCHARIDE NAG B1628 BOUND TO ASN B 327
30DC3SOFTWAREILE A:555 , GLU A:558 , ACT A:1627 , HOH A:2357 , HOH A:2359 , ASN B:396 , CYS B:397 , SER B:398 , ARG B:399 , SO4 B:1622 , HOH B:2107BINDING SITE FOR MONO-SACCHARIDE NAG B1627 BOUND TO ASN B 396
31DC4SOFTWAREASN C:142 , SER C:144 , GLY C:147 , ASN C:150BINDING SITE FOR MONO-SACCHARIDE NAG C1173 BOUND TO ASN C 142
32DC5SOFTWARETYR E:37 , ASN E:39 , SER E:41 , HOH E:2011 , HOH E:2035BINDING SITE FOR MONO-SACCHARIDE NAG E1175 BOUND TO ASN E 39
33DC6SOFTWAREASN E:142 , SER E:144 , GLU E:146 , GLY E:147 , ASN E:150BINDING SITE FOR MONO-SACCHARIDE NAG E1174 BOUND TO ASN E 142

(-) SS Bonds  (20, 20)

Asymmetric Unit
No.Residues
1A:205 -A:611
2A:232 -A:256
3A:298 -A:311
4A:378 -A:422
5A:392 -A:405
6A:397 -A:509
7A:503 -A:513
8A:575 -A:584
9B:205 -B:611
10B:232 -B:256
11B:298 -B:311
12B:378 -B:422
13B:392 -B:405
14B:397 -B:509
15B:503 -B:513
16B:575 -B:584
17C:65 -C:104
18C:92 -C:156
19E:65 -E:104
20E:92 -E:156

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4UF7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UF7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UF7)

(-) Exons   (0, 0)

(no "Exon" information available for 4UF7)

(-) Sequences/Alignments

Asymmetric 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:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee...........eeeeeeeeeee..eeeeeeeeee.hhhhh.eeeeeeeeeeeee.....eeee...eee..hhh.eeeeeeee...eeeeeeee....hhhhhhhhhh.eeeeeeee.....eeeeee.hhhee...eeeeee.eee.eee..eeeeeeeeee.................hhhhhhhhh..........eeeeeeeee.......eeeeee...........eeeeee..eeeeee.........eeeeeeehhhheeee...............................eee.......eeeeee........eeeeee....eeeeee....eeeeeeeeeeeeee..eeeeeeeeeeee....ee..eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uf7 A 201 GPSPCRNFSSVPTIYYYRIPGLYNRTALDERCILNPRLTISSTKFAYVHSEYDKNCTRGFKYYELMTFGEILEGPEKEPRMFSRSFYSPTNAVNYHSCTPIVTVNEGYFLCLECTSSDPLYKANLSNSTFHLVILRHNKDEKIVSMPSFNLSTDQEYVQIIPAEGGGTAESGNLYFPCIGRLLHKRVTHPLCKKSNCSRTDDESCLKSYYNQGSPQHQVVNCLIRIRNAQRDNPTWDVITVDLTNTYPGSRSRIFGSFSKPMLYQSSVSWHTLLQVAEITDLDKYQLDWLDTPYISRPGGSECPFGNYCPTVCWEGTYNDVYSLTPNNDLFVTVYLKSEQVAENPYFAIFSRDQILKEFPLDAWISSARTTTISCFMFNNEIWCIAALEITRLNDDIIRPIYYSFWLPTDCRTPYPH 617
                                   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       


Chain B from PDB  Type:PROTEIN  Length:412
                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee...........eeeeeeeeeee..eeeeeeeeee.hhhhh.eeeeeeeeeeeee.....eeee........hhh.eeeeeeee....eeeeeee....hhhhhhhhhh.eeeeeee......eeeeee.hhhee...eeeeee.eee.eee..eeeeeeeeee.................hhhhhhhhh..........eeeeeeeee...eeeeee...........eeeeee..eeeeee.........eeeeeeehhhheeee...............................eee.......eeeeee........eeeeee....eeeeee....eeeeeeeeeeeeee..eeeeeeeeeeee....ee..eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uf7 B 202 PSPCRNFSSVPTIYYYRIPGLYNRTALDERCILNPRLTISSTKFAYVHSEYDKNCTRGFKYYELMTFGEILEGPEKEPRMFSRSFYSPTNAVNYHSCTPIVTVNEGYFLCLECTSSDPLYKANLSNSTFHLVILRHNKDEKIVSMPSFNLSTDQEYVQIIPAEGGGTAESGNLYFPCIGRLLHKRVTHPLCKKSNCSRTDDESCLKSYYNQGSPQHQVVNCLIRIRNAPTWDVITVDLTNTYPGSRSRIFGSFSKPMLYQSSVSWHTLLQVAEITDLDKYQLDWLDTPYISRPGGSECPFGNYCPTVCWEGTYNDVYSLTPNNDLFVTVYLKSEQVAENPYFAIFSRDQILKEFPLDAWISSARTTTISCFMFNNEIWCIAALEITRLNDDIIRPIYYSFWLPTDCRTPYPH 617
                                   211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615  
                                                                                                                                                                                                                                                             429|                                                                                                                                                                                       
                                                                                                                                                                                                                                                              434                                                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.............eee......eeeeee.........eeeeeehhhhhhh..........eee......eeeeee................eeeeee.....hhhhh....hhhhhhh..eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4uf7 C  30 SIVLEPIYWNSSNSKFLPGQGLVLYPQIGDKLDIICPKVDGQYEYYKVYMVDKDQADRCTIKKENTPLLNCAKPDQDIKFTIKFQEFSPNLWGLEFQKNKDYYIISTSNGSLEGLDNQEGGVCQTRAMKILMKVGQDG 171
                                    39        49        59        69|       83        93       103       113       123       133       143       153       163        
                                                                  69|                                                                                                 
                                                                   74                                                                                                 


Chain E from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.............eee.....eeeeeee.........eeeeeehhhhhhh..........eee......eeeeee................eeeeee.....hhhhh....hhhhhhh..eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uf7 E  30 SIVLEPIYWNSSNSKFLPGQGLVLYPQIGDKLDIICPKVDGQYEYYKVYMVDKDQADRCTIKKENTPLLNCAKPDQDIKFTIKFQEFSPNLWGLEFQKNKDYYIISTSNGSLEGLDNQEGGVCQTRAMKILMKVGQDGT 172
                                    39        49        59        69|       83        93       103       113       123       133       143       153       163         
                                                                  69|                                                                                                  
                                                                   74
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  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  (0, 0)

(no "SCOP Domain" information available for 4UF7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UF7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UF7)

(-) Gene Ontology  (32, 34)

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 Related Entries

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        EFNB2_HUMAN | P52799: 2hle 2i85 2vsk 2vsm 2wo2 3gxu

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