3KXU - JenaLib

Title :   CRYSTAL STRUCTURE OF HUMAN FERRITIN FTL498INSTC PATHOGENIC MUTANT

Authors :   T. Granier, B. Gallois, B. Langlois D'Estaintot, P. Arosio

Date :   04 Dec 09 (Deposition) - 09 Feb 10 (Release) - 19 May 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A
Biol. Unit 1: A  (24x)

Keywords :   Iron Storage Protein, Disorder, Iron, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Luscieti, P. Santambrogio, B. Langlois D'Estaintot, T. Granier, A. Cozzi, M. Poli, B. Gallois, D. Finazzi, A. Cattaneo, S. Levi, P. Arosio
Mutant Ferritin L-Chains That Cause Neurodegeneration Act In A Dominant-Negative Manner To Reduce Ferritin Iron Incorporation.
J. Biol. Chem. V. 285 11948 2010
PubMed-ID: 20159981 | Reference-DOI: 10.1074/JBC.M109.096404

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (13, 13)

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:115 , CYS A:127 , HOH A:192 , HOH A:193 , HOH A:194 , HOH A:215	BINDING SITE FOR RESIDUE CD A 301
02	AC2	SOFTWARE	HIS A:50 , GLU A:54 , HOH A:220 , CD A:304	BINDING SITE FOR RESIDUE CD A 302
03	AC3	SOFTWARE	HIS A:50 , CD A:302	BINDING SITE FOR RESIDUE CD A 304
04	AC4	SOFTWARE	GLU A:54 , GLU A:57 , HOH A:221 , HOH A:222 , HOH A:223	BINDING SITE FOR RESIDUE CD A 305
05	AC5	SOFTWARE	GLU A:58 , GLU A:61 , HOH A:224 , HOH A:225	BINDING SITE FOR RESIDUE CD A 306
06	AC6	SOFTWARE	GLU A:89 , HOH A:226 , HOH A:227	BINDING SITE FOR RESIDUE CD A 308
07	AC7	SOFTWARE	HIS A:133 , HOH A:228 , HOH A:229 , HOH A:230 , HOH A:231 , HOH A:232	BINDING SITE FOR RESIDUE CD A 309
08	AC8	SOFTWARE	GLU A:87 , HOH A:233 , HOH A:234 , HOH A:235	BINDING SITE FOR RESIDUE CD A 312
09	AC9	SOFTWARE	CYS A:127 , ASP A:128 , GLU A:131	BINDING SITE FOR RESIDUE CD A 313
10	BC1	SOFTWARE	ASP A:128	BINDING SITE FOR RESIDUE CD A 314
11	BC2	SOFTWARE	ASP A:12 , HOH A:236 , HOH A:237	BINDING SITE FOR RESIDUE CD A 315
12	BC3	SOFTWARE	HIS A:153 , HOH A:238 , HOH A:239	BINDING SITE FOR RESIDUE CD A 316
13	BC4	SOFTWARE	SER A:10 , ASP A:12 , ARG A:121 , HOH A:237 , HOH A:345 , HOH A:346 , HOH A:381 , HOH A:419 , HOH A:423	BINDING SITE FOR RESIDUE SO4 A 317

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (3, 3)

Exons (0, 0)

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:156
 aligned with FRIL_HUMAN | P02792 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
           FRIL_HUMAN     2 SSQIRQNYSTDVEAAVNSLVNLYLQASYTYLSLGFYFDRDDVALEGVSHFFRELAEEKREGYERLLKMQNQRGGRALFQDIKKPAEDEWGKTPDAMKAAMALEKKLNQALLDLHALGSARTDPHLCDFLETHFLDEEVKLIKKMGDHLTNLHRLGG 157
               SCOP domains d3kxua_ A: (Apo)ferritin                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------Ferritin-3kxuA01 A:14-155                                                                                                                     -- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------I-----------------------------------------------------------------T------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----FERRITIN_LIKE  PDB: A:7-156 UniProt: 7-156                                                                                                            - PROSITE (1)
                PROSITE (2) --------------------------------------------------------FERRITIN_1         ----------------------------------------------FERRITIN_2           -------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kxu A   2 SSQIRQNYSTDVEAAVNSLVNLYLQASYTYLSLGFYFDRDDVALEGVSHFFRELAEEKREGYERLLKMQNQRGGRALFQDIKKPAEDEWGKTPDAMKAAMALEKKLNQALLDLHALGSARTDPHLCDFLETHFLDEEVKLIKKMGDHLTNLHRLGG 157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain A from PDB  Type:PROTEIN  Length:156
 aligned with Q6S4P3_HUMAN | Q6S4P3 from UniProtKB/TrEMBL  Length:191

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
         Q6S4P3_HUMAN     2 SSQIRQNYSTDVEAAVNSLVNLYLQASYTYLSLGFYFDRDDVALEGVSHFFRELAEEKREGYERLLKMQNQRGGRALFQDIKKPAEDEWGKTPDAMKAAMALEKKLNQALLDLHALGSARTDPHLCDFLETHFLDEEVKLIKKMGDHLTNLHRLGG 157
               SCOP domains d3kxua_ A: (Apo)ferritin                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------Ferritin-3kxuA01 A:14-155                                                                                                                     -- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------I-----------------------------------------------------------------T------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kxu A   2 SSQIRQNYSTDVEAAVNSLVNLYLQASYTYLSLGFYFDRDDVALEGVSHFFRELAEEKREGYERLLKMQNQRGGRALFQDIKKPAEDEWGKTPDAMKAAMALEKKLNQALLDLHALGSARTDPHLCDFLETHFLDEEVKLIKKMGDHLTNLHRLGG 157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (13, 17)

Asymmetric Unit(hide GO term definitions)

Chain A (FRIL_HUMAN | P02792)

molecular function
	GO:0008199	ferric iron binding	Interacting selectively and non-covalently with ferric iron, Fe(III).
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006879	cellular iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
	GO:0055072	iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
	GO:0006826	iron ion transport	The directed movement of iron (Fe) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0008043	intracellular ferritin complex	A ferritin complex located in the cell. Intracellular ferritin complexes contain 24 subunits, in a mixture of L (light) chains and H (heavy) chains.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A (Q6S4P3_HUMAN | Q6S4P3)

molecular function
	GO:0008199	ferric iron binding	Interacting selectively and non-covalently with ferric iron, Fe(III).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006879	cellular iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
	GO:0006826	iron ion transport	The directed movement of iron (Fe) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
	GO:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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
		CD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ 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 ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3kxu)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3kxu
		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
	FRIL_HUMAN \| P02792
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	Q6S4P3_HUMAN \| Q6S4P3
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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)
	600886
		Disease Information	:	OMIM
	606159
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description