Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4KDT

Structure of an early native-like intermediate of beta2-microglobulin amyloidosis

Functional Information from GO Data

Chain	GOid	namespace	contents
C	0000139	cellular_component	Golgi membrane
C	0001913	biological_process	T cell mediated cytotoxicity
C	0001916	biological_process	positive regulation of T cell mediated cytotoxicity
C	0002237	biological_process	response to molecule of bacterial origin
C	0002474	biological_process	antigen processing and presentation of peptide antigen via MHC class I
C	0002481	biological_process	antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent
C	0002502	biological_process	peptide antigen assembly with MHC class I protein complex
C	0002503	biological_process	peptide antigen assembly with MHC class II protein complex
C	0002726	biological_process	positive regulation of T cell cytokine production
C	0005198	molecular_function	structural molecule activity
C	0005515	molecular_function	protein binding
C	0005576	cellular_component	extracellular region
C	0005615	cellular_component	extracellular space
C	0005765	cellular_component	lysosomal membrane
C	0005783	cellular_component	endoplasmic reticulum
C	0005788	cellular_component	endoplasmic reticulum lumen
C	0005794	cellular_component	Golgi apparatus
C	0005829	cellular_component	cytosol
C	0005886	cellular_component	plasma membrane
C	0005925	cellular_component	focal adhesion
C	0006826	biological_process	iron ion transport
C	0006879	biological_process	intracellular iron ion homeostasis
C	0006955	biological_process	immune response
C	0007608	biological_process	sensory perception of smell
C	0007611	biological_process	learning or memory
C	0009897	cellular_component	external side of plasma membrane
C	0009986	cellular_component	cell surface
C	0010977	biological_process	negative regulation of neuron projection development
C	0012507	cellular_component	ER to Golgi transport vesicle membrane
C	0016020	cellular_component	membrane
C	0019885	biological_process	antigen processing and presentation of endogenous peptide antigen via MHC class I
C	0019886	biological_process	antigen processing and presentation of exogenous peptide antigen via MHC class II
C	0023026	molecular_function	MHC class II protein complex binding
C	0030670	cellular_component	phagocytic vesicle membrane
C	0031901	cellular_component	early endosome membrane
C	0031902	cellular_component	late endosome membrane
C	0031905	cellular_component	early endosome lumen
C	0032092	biological_process	positive regulation of protein binding
C	0033077	biological_process	T cell differentiation in thymus
C	0034756	biological_process	regulation of iron ion transport
C	0035580	cellular_component	specific granule lumen
C	0042026	biological_process	protein refolding
C	0042605	molecular_function	peptide antigen binding
C	0042612	cellular_component	MHC class I protein complex
C	0042613	cellular_component	MHC class II protein complex
C	0042802	molecular_function	identical protein binding
C	0042803	molecular_function	protein homodimerization activity
C	0042824	cellular_component	MHC class I peptide loading complex
C	0045646	biological_process	regulation of erythrocyte differentiation
C	0048260	biological_process	positive regulation of receptor-mediated endocytosis
C	0050680	biological_process	negative regulation of epithelial cell proliferation
C	0050768	biological_process	negative regulation of neurogenesis
C	0050778	biological_process	positive regulation of immune response
C	0050870	biological_process	positive regulation of T cell activation
C	0051289	biological_process	protein homotetramerization
C	0055038	cellular_component	recycling endosome membrane
C	0060586	biological_process	multicellular organismal-level iron ion homeostasis
C	0070062	cellular_component	extracellular exosome
C	0071281	biological_process	cellular response to iron ion
C	0071283	biological_process	cellular response to iron(III) ion
C	0071316	biological_process	cellular response to nicotine
C	1900121	biological_process	negative regulation of receptor binding
C	1900122	biological_process	positive regulation of receptor binding
C	1904434	biological_process	positive regulation of ferrous iron binding
C	1904437	biological_process	positive regulation of transferrin receptor binding
C	1904724	cellular_component	tertiary granule lumen
C	1990000	biological_process	amyloid fibril formation
C	1990712	cellular_component	HFE-transferrin receptor complex
C	2000774	biological_process	positive regulation of cellular senescence
C	2000978	biological_process	negative regulation of forebrain neuron differentiation
D	0000139	cellular_component	Golgi membrane
D	0001913	biological_process	T cell mediated cytotoxicity
D	0001916	biological_process	positive regulation of T cell mediated cytotoxicity
D	0002237	biological_process	response to molecule of bacterial origin
D	0002474	biological_process	antigen processing and presentation of peptide antigen via MHC class I
D	0002481	biological_process	antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent
D	0002502	biological_process	peptide antigen assembly with MHC class I protein complex
D	0002503	biological_process	peptide antigen assembly with MHC class II protein complex
D	0002726	biological_process	positive regulation of T cell cytokine production
D	0005198	molecular_function	structural molecule activity
D	0005515	molecular_function	protein binding
D	0005576	cellular_component	extracellular region
D	0005615	cellular_component	extracellular space
D	0005765	cellular_component	lysosomal membrane
D	0005783	cellular_component	endoplasmic reticulum
D	0005788	cellular_component	endoplasmic reticulum lumen
D	0005794	cellular_component	Golgi apparatus
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
D	0005925	cellular_component	focal adhesion
D	0006826	biological_process	iron ion transport
D	0006879	biological_process	intracellular iron ion homeostasis
D	0006955	biological_process	immune response
D	0007608	biological_process	sensory perception of smell
D	0007611	biological_process	learning or memory
D	0009897	cellular_component	external side of plasma membrane
D	0009986	cellular_component	cell surface
D	0010977	biological_process	negative regulation of neuron projection development
D	0012507	cellular_component	ER to Golgi transport vesicle membrane
D	0016020	cellular_component	membrane
D	0019885	biological_process	antigen processing and presentation of endogenous peptide antigen via MHC class I
D	0019886	biological_process	antigen processing and presentation of exogenous peptide antigen via MHC class II
D	0023026	molecular_function	MHC class II protein complex binding
D	0030670	cellular_component	phagocytic vesicle membrane
D	0031901	cellular_component	early endosome membrane
D	0031902	cellular_component	late endosome membrane
D	0031905	cellular_component	early endosome lumen
D	0032092	biological_process	positive regulation of protein binding
D	0033077	biological_process	T cell differentiation in thymus
D	0034756	biological_process	regulation of iron ion transport
D	0035580	cellular_component	specific granule lumen
D	0042026	biological_process	protein refolding
D	0042605	molecular_function	peptide antigen binding
D	0042612	cellular_component	MHC class I protein complex
D	0042613	cellular_component	MHC class II protein complex
D	0042802	molecular_function	identical protein binding
D	0042803	molecular_function	protein homodimerization activity
D	0042824	cellular_component	MHC class I peptide loading complex
D	0045646	biological_process	regulation of erythrocyte differentiation
D	0048260	biological_process	positive regulation of receptor-mediated endocytosis
D	0050680	biological_process	negative regulation of epithelial cell proliferation
D	0050768	biological_process	negative regulation of neurogenesis
D	0050778	biological_process	positive regulation of immune response
D	0050870	biological_process	positive regulation of T cell activation
D	0051289	biological_process	protein homotetramerization
D	0055038	cellular_component	recycling endosome membrane
D	0060586	biological_process	multicellular organismal-level iron ion homeostasis
D	0070062	cellular_component	extracellular exosome
D	0071281	biological_process	cellular response to iron ion
D	0071283	biological_process	cellular response to iron(III) ion
D	0071316	biological_process	cellular response to nicotine
D	1900121	biological_process	negative regulation of receptor binding
D	1900122	biological_process	positive regulation of receptor binding
D	1904434	biological_process	positive regulation of ferrous iron binding
D	1904437	biological_process	positive regulation of transferrin receptor binding
D	1904724	cellular_component	tertiary granule lumen
D	1990000	biological_process	amyloid fibril formation
D	1990712	cellular_component	HFE-transferrin receptor complex
D	2000774	biological_process	positive regulation of cellular senescence
D	2000978	biological_process	negative regulation of forebrain neuron differentiation

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 201

Chain	Residue
A	ASP106
A	ILE107
A	GLY112
A	ASP113
A	GLY114

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 202

Chain	Residue
D	LYS94
A	TYR59
A	LYS65
A	LYS110
A	HOH306

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 A 203

Chain	Residue
A	SER25
A	GLY26
A	SER30

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 B 201

Chain	Residue
B	TYR59
B	LYS65
B	LYS110
C	LYS94

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 101

Chain	Residue
B	ARG31
B	SER53
C	ARG45
C	ARG81

site_id	AC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL C 102

Chain	Residue
C	ARG12
C	ARG12

site_id	AC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 D 101

Chain	Residue
A	ARG31
D	ARG45
D	ARG81

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL D 102

Chain	Residue
D	TYR26
D	SER52
D	TYR63

Functional Information from PROSITE/UniProt

site_id	PS00290
Number of Residues	7
Details	IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YACRVNH

Chain	Residue	Details
C	TYR78-HIS84

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	MOD_RES: Pyrrolidone carboxylic acid; in form pI 5.3 => ECO:0000269\|PubMed:7554280

Chain	Residue	Details
C	GLN2
D	GLN2

site_id	SWS_FT_FI2
Number of Residues	2
Details	CARBOHYD: N-linked (Glc) (glycation) isoleucine; in hemodialysis-associated amyloidosis => ECO:0000269\|PubMed:7918443

Chain	Residue	Details
C	ILE1
D	ILE1

site_id	SWS_FT_FI3
Number of Residues	12
Details	CARBOHYD: N-linked (Glc) (glycation) lysine; in vitro => ECO:0000269\|PubMed:7918443

Chain	Residue	Details
C	LYS19
D	LYS58
D	LYS91
D	LYS94
C	LYS41
C	LYS48
C	LYS58
C	LYS91
C	LYS94
D	LYS19
D	LYS41
D	LYS48

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)