Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HEMAGGLUTININ FROM AN H7N9 INFLUENZA VIRUS IN COMPLEX WITH A SULFATED RECEPTOR ANALOG
 
Authors :  R. Xu, I. A. Wilson
Date :  11 Oct 13  (Deposition) - 18 Dec 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (3x)
Biol. Unit 2:  C,D  (3x)
Keywords :  Viral Envelope Protein, Hemagglutinin, Viral Fusion Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Xu, R. P. De Vries, X. Zhu, C. M. Nycholat, R. Mcbride, W. Yu, J. C. Paulson, I. A. Wilson
Preferential Recognition Of Avian-Like Receptors In Human Influenza A H7N9 Viruses.
Science V. 342 1230 2013
PubMed-ID: 24311689  |  Reference-DOI: 10.1126/SCIENCE.1243761

(-) Compounds

Molecule 1 - HEMAGGLUTININ HA1
    Chains: A, C
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Plasmid: PFASTBAC-HT
    Expression System Strain: HI5
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: HA, HEMAGGLUTININ
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 1332244
    Strain: A/SHANGHAI/2/2013
 
Molecule 2 - HEMAGGLUTININ HA2
    Chains: B, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Plasmid: PFASTBAC-HT
    Expression System Strain: HI5
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: HA, HEMAGGLUTININ
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 1332244
    Strain: A/SHANGHAI/2/2013

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): AB  
Biological Unit 2 (3x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric Unit (5, 11)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NGS2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-6-O-SULFO-BETA-D-GLUCOPYRANOSE
5SIA2Ligand/IonO-SIALIC ACID
Biological Unit 1 (5, 24)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2GAL3Ligand/IonBETA-D-GALACTOSE
3NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NGS3Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-6-O-SULFO-BETA-D-GLUCOPYRANOSE
5SIA3Ligand/IonO-SIALIC ACID
Biological Unit 2 (3, 9)
No.NameCountTypeFull Name
1BMA-1Ligand/IonBETA-D-MANNOSE
2GAL3Ligand/IonBETA-D-GALACTOSE
3NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NGS3Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-6-O-SULFO-BETA-D-GLUCOPYRANOSE
5SIA3Ligand/IonO-SIALIC ACID

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:38 , THR A:318 , NAG A:402 , LEU B:52BINDING SITE FOR RESIDUE NAG A 401
02AC2SOFTWARETHR A:40 , NAG A:401 , BMA A:403BINDING SITE FOR RESIDUE NAG A 402
03AC3SOFTWARENAG A:402BINDING SITE FOR RESIDUE BMA A 403
04AC4SOFTWARELYS A:169 , ASN A:240BINDING SITE FOR RESIDUE NAG A 404
05AC5SOFTWARETYR A:98 , GLY A:134 , ALA A:135 , THR A:136 , SER A:137 , HIS A:183 , GLU A:190 , LEU A:194 , GAL A:406BINDING SITE FOR RESIDUE SIA A 405
06AC6SOFTWARESIA A:405 , NGS A:407BINDING SITE FOR RESIDUE GAL A 406
07AC7SOFTWAREVAL A:186 , GLU A:190 , GLN A:222 , GLY A:225 , LEU A:226 , SER A:227 , GAL A:406BINDING SITE FOR RESIDUE NGS A 407
08AC8SOFTWAREGLU B:72 , LYS B:75 , GLY B:78 , ASN B:79 , ASN B:82 , HOH B:322BINDING SITE FOR RESIDUE NAG B 201
09AC9SOFTWARETYR C:98 , ALA C:135 , THR C:136 , SER C:137 , LEU C:155 , HIS C:183 , GLU C:190 , LEU C:194 , GAL C:402BINDING SITE FOR RESIDUE SIA C 401
10BC1SOFTWARESIA C:401 , NGS C:403BINDING SITE FOR RESIDUE GAL C 402
11BC2SOFTWAREVAL C:186 , GLU C:190 , GLN C:222 , GLY C:225 , LEU C:226 , SER C:227 , GAL C:402BINDING SITE FOR RESIDUE NGS C 403

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:14 -B:137
2A:52 -A:277
3A:64 -A:76
4A:97 -A:139
5A:281 -A:305
6B:144 -B:148
7C:14 -D:137
8C:52 -C:277
9C:64 -C:76
10C:97 -C:139
11C:281 -C:305
12D:144 -D:148

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N62)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N62)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N62)

(-) Exons   (0, 0)

(no "Exon" information available for 4N62)

(-) 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:318
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4n62a_ A: automated matches                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee......eeee....eeeee..eee.ee......ee.....eee......hhhhhhhhhhhhhh.....eeee..........eee.hhhhhhhhhhh...eeeee...........................eee............eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeee....eeee....ee......eee..ee......ee......ee...ee......eee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4n62 A   11 DKICLGHHAVSNGTKVNTLTERGVEVVNATETVERTNIPRICSKGKRTVDLGQCGLLGTITGPPQCDQFLEFSADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKEAMGFTYSGIRTNGATSACRRSGSSFYAEMKWLLSNTDNAAFPQMTKSYKNTRKSPALIVWGIHHSVSTAEQTKLYGSGNKLVTVGSSNYQQSFVPSPGARPQVNGLSGRIDFHWLMLNPNDTVTFSFNGAFIAPDRASFLRGKSMGIQSGVQVDANCEGDCYHSGGTIISNLPFQNIDSRAVGKCPRYVKQRSLLLATGMKNVPEIP  327
                                    20        30        40        50        60        70        80        90       100       110       120       130       140||     151       159       169       179       189       199       209       219       229       239       249       259   ||  270      |279       289       299       309       319        
                                                                                                                                                            141|            158A|                                                                                                      263|        276A                                                   
                                                                                                                                                             143             158B                                                                                                       265                                                               


Chain B from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                          
               SCOP domains d4n62b_ B: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4n62 B    4 GAIAGFIENGWEGLIDGWYGFRHQNAQGEGTAADYKSTQSAIDQITGKLNRLIEKTNQQFELIDNEFNEVEKQIGNVINWTRDSITEVWSYNAELLVAMENQHTIDLADSEMDKLYERVKRQLRENAEEDGTGCFEIFHKCDDDCMASIRNNTYDHSKYREEAMQNRIQ  172
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163         


Chain C from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4n62c_ C: automated matches                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee......eeee....eeeee..eee.ee......ee.....eee......hhhhhhhhhhhhhh.....eeee..........eee.hhhhhhhhhhh...eeeee.............hhhhh.........eee............eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeee....eeee....ee......eee..ee......ee......ee...ee......eee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4n62 C   11 DKICLGHHAVSNGTKVNTLTERGVEVVNATETVERTNIPRICSKGKRTVDLGQCGLLGTITGPPQCDQFLEFSADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKEAMGFTYSGIRTNGATSACRRSGSSFYAEMKWLLSNTDNAAFPQMTKSYKNTRKSPALIVWGIHHSVSTAEQTKLYGSGNKLVTVGSSNYQQSFVPSPGARPQVNGLSGRIDFHWLMLNPNDTVTFSFNGAFIAPDRASFLRGKSMGIQSGVQVDANCEGDCYHSGGTIISNLPFQNIDSRAVGKCPRYVKQRSLLLATGMKNVPEIP  327
                                    20        30        40        50        60        70        80        90       100       110       120       130       140||     151       159       169       179       189       199       209       219       229       239       249       259   ||  270      |279       289       299       309       319        
                                                                                                                                                            141|            158A|                                                                                                      263|        276A                                                   
                                                                                                                                                             143             158B                                                                                                       265                                                               


Chain D from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                          
               SCOP domains d4n62d_ D: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4n62 D    4 GAIAGFIENGWEGLIDGWYGFRHQNAQGEGTAADYKSTQSAIDQITGKLNRLIEKTNQQFELIDNEFNEVEKQIGNVINWTRDSITEVWSYNAELLVAMENQHTIDLADSEMDKLYERVKRQLRENAEEDGTGCFEIFHKCDDDCMASIRNNTYDHSKYREEAMQNRIQ  172
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N62)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N62)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NGS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SIA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4n62)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4n62
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  R4NN21_9INFA | R4NN21
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  R4NN21_9INFA | R4NN21
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        R4NN21_9INFA | R4NN21: 5vjk 5vjl 5vjm
UniProtKB/TrEMBL
        R4NN21_9INFA | R4NN21: 4ln3 4ln4 4ln6 4ln8 4n5j 4n5k 4n60 4n61 4n63 4n64 5t6s

(-) Related Entries Specified in the PDB File

4n5j 4n5k 4n60 4n61 4n63 4n64