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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NEGATIVELY SUPERCHARGED VARIANT FTN(NEG) OF HUMAN HEAVY CHAIN FERRITIN
 
Authors :  M. Kuenzle, T. Beck
Date :  26 Apr 16  (Deposition) - 10 May 17  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D,E,F,G,H  (3x)
Keywords :  Protein Design, Protein Engineering, Charged Protein Containers, Binary Protein Structures, Self-Assembly, Binary Nanoparticle Superlattices, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kuenzle, T. Eckert, T. Beck
Self-Assembly Of Charged Protein Containers Enables Positioning Of Nanoparticles In A 3-D Lattice To Form Biohybrid Materials
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FERRITIN HEAVY CHAIN
    Chains: A, B, C, D, E, F, G, H
    EC Number: 1.16.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FTH1, FTH, FTHL6, OK/SW-CL.84, PIG15
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FERRITIN H SUBUNIT,CELL PROLIFERATION-INDUCING GENE 15 PROTEIN,NEGATIVELY CHARGED VARIANT OF HUMAN HEAVY CHAIN FERRITIN

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (3x): ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 29)

Asymmetric Unit (3, 29)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FE10Ligand/IonFE (III) ION
3MG17Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE-1Ligand/IonFE (III) ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:27 , GLU A:62 , HIS A:65 , HOH A:311 , HOH A:334 , HOH A:343binding site for residue FE A 201
02AC2SOFTWAREHIS A:173 , CL A:205 , HIS C:173 , HIS F:173 , HIS G:173binding site for residue FE A 202
03AC3SOFTWAREGLN A:58 , HOH A:315 , HOH A:347 , HOH A:407 , HOH A:503binding site for residue MG A 203
04AC4SOFTWAREASP A:131 , HOH A:329 , HOH A:373binding site for residue MG A 204
05AC5SOFTWAREHIS A:173 , FE A:202 , HIS C:173 , HIS F:173 , HIS G:173binding site for residue CL A 205
06AC6SOFTWAREGLU B:27 , GLU B:62 , HIS B:65 , HOH B:309 , HOH B:334binding site for residue FE B 201
07AC7SOFTWAREGLN B:58 , GLU B:61 , HOH B:301 , HOH B:340 , HOH B:389 , HOH B:484binding site for residue MG B 202
08AC8SOFTWAREHOH B:333 , HOH B:491 , HOH C:345 , HOH C:486 , HOH D:337 , HOH D:480binding site for residue MG B 203
09AC9SOFTWAREGLU C:27 , GLU C:62 , HIS C:65 , HOH C:313 , HOH C:331 , HOH C:344binding site for residue FE C 201
10AD1SOFTWAREGLN C:58 , GLU C:61 , HOH C:317 , HOH C:386 , HOH C:389binding site for residue MG C 202
11AD2SOFTWAREASP B:131 , HOH B:327 , HOH B:330 , ASP C:131 , HOH C:339 , ASP D:131 , HOH D:308 , HOH D:322 , HOH D:372binding site for residue MG C 203
12AD3SOFTWAREASP C:84 , HOH C:403 , HOH H:343binding site for residue MG C 204
13AD4SOFTWAREGLU D:27 , GLU D:62 , HIS D:65 , HOH D:312 , HOH D:325binding site for residue FE D 201
14AD5SOFTWAREHIS B:173 , HIS D:173 , CL D:205 , HIS E:173 , HIS H:173binding site for residue FE D 202
15AD6SOFTWAREGLN D:58 , HOH D:305 , HOH D:323 , HOH D:394 , HOH D:497binding site for residue MG D 203
16AD7SOFTWAREASP D:84 , HOH D:375 , HOH D:452binding site for residue MG D 204
17AD8SOFTWAREHIS B:173 , HIS D:173 , FE D:202 , HIS E:173 , HIS H:173binding site for residue CL D 205
18AD9SOFTWAREGLU E:27 , GLU E:62 , HIS E:65 , HOH E:314 , HOH E:323binding site for residue FE E 201
19AE1SOFTWAREGLN E:58 , GLU E:61 , HOH E:302 , HOH E:310 , HOH E:409binding site for residue MG E 202
20AE2SOFTWAREHOH E:321 , HOH E:484binding site for residue MG E 203
21AE3SOFTWAREHOH B:325 , ASP E:84 , HOH E:411binding site for residue MG E 204
22AE4SOFTWAREGLU F:27 , GLU F:62 , HIS F:65 , HOH F:308 , HOH F:345binding site for residue FE F 201
23AE5SOFTWAREGLN F:58 , HOH F:302 , HOH F:404 , HOH F:502binding site for residue MG F 202
24AE6SOFTWAREHOH F:339 , HOH F:489 , HOH G:331 , HOH G:478 , HOH H:328 , HOH H:483binding site for residue MG F 203
25AE7SOFTWAREASP F:84 , HOH F:334 , HOH F:462binding site for residue MG F 204
26AE8SOFTWAREGLU G:27 , GLU G:62 , HIS G:65 , HOH G:315 , HOH G:334binding site for residue FE G 201
27AE9SOFTWAREGLN G:58 , HOH G:311 , HOH G:372 , HOH G:397 , HOH G:493binding site for residue MG G 202
28AF1SOFTWAREGLU H:27 , GLU H:62 , HIS H:65 , HOH H:329 , HOH H:333binding site for residue FE H 201
29AF2SOFTWAREGLN H:58 , GLU H:61 , HOH H:304 , HOH H:309binding site for residue MG H 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JKK)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ala A:160 -Pro A:161
2Ala B:160 -Pro B:161
3Ala C:160 -Pro C:161
4Ala D:160 -Pro D:161
5Ala E:160 -Pro E:161
6Ala F:160 -Pro F:161
7Ala G:160 -Pro G:161
8Ala H:160 -Pro H:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JKK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JKK)

(-) Exons   (0, 0)

(no "Exon" information available for 5JKK)

(-) 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:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jkk A   5 TSQVRQNYHQDSEEAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIQKPDEDDWESGLNAMEEALELEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLG 176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  


Chain B from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jkk B   5 TSQVRQNYHQDSEEAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIQKPDEDDWESGLNAMEEALELEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLG 176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  


Chain C from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jkk C   5 TSQVRQNYHQDSEEAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIQKPDEDDWESGLNAMEEALELEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLG 176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  


Chain D from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jkk D   5 TSQVRQNYHQDSEEAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIQKPDEDDWESGLNAMEEALELEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLG 176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  


Chain E from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jkk E   5 TSQVRQNYHQDSEEAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIQKPDEDDWESGLNAMEEALELEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLG 176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  


Chain F from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jkk F   5 TSQVRQNYHQDSEEAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIQKPDEDDWESGLNAMEEALELEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLG 176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  


Chain G from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jkk G   5 TSQVRQNYHQDSEEAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIQKPDEDDWESGLNAMEEALELEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLG 176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  


Chain H from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jkk H   5 TSQVRQNYHQDSEEAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIQKPDEDDWESGLNAMEEALELEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLG 176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
   Legend:   → Mismatch (orange background)
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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 5JKK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JKK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JKK)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Ala D:160 - Pro D:161   [ RasMol ]  
    Ala E:160 - Pro E:161   [ RasMol ]  
    Ala F:160 - Pro F:161   [ RasMol ]  
    Ala G:160 - Pro G:161   [ RasMol ]  
    Ala H:160 - Pro H:161   [ RasMol ]  
 
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  5jkk
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  1.16.3.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        FRIH_HUMAN | P02794: 1fha 2cei 2chi 2cih 2clu 2cn6 2cn7 2fha 2iu2 2z6m 3ajo 3ajp 3ajq 3erz 3es3 4dyx 4dyy 4dyz 4dz0 4oyn 4y08 4ykh 4zjk 5cmq 5cmr 5gn8 5gou 5jkl 5jkm 5up7 5up8 5vtd

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5JKK)