4U1L

HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes

Functional Information from GO Data

Chain	GOid	namespace	contents
B	0000139	cellular_component	Golgi membrane
B	0001913	biological_process	T cell mediated cytotoxicity
B	0001916	biological_process	positive regulation of T cell mediated cytotoxicity
B	0002237	biological_process	response to molecule of bacterial origin
B	0002376	biological_process	immune system process
B	0002474	biological_process	antigen processing and presentation of peptide antigen via MHC class I
B	0002481	biological_process	antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent
B	0002502	biological_process	peptide antigen assembly with MHC class I protein complex
B	0002503	biological_process	peptide antigen assembly with MHC class II protein complex
B	0002726	biological_process	positive regulation of T cell cytokine production
B	0005198	molecular_function	structural molecule activity
B	0005515	molecular_function	protein binding
B	0005576	cellular_component	extracellular region
B	0005615	cellular_component	extracellular space
B	0005765	cellular_component	lysosomal membrane
B	0005783	cellular_component	endoplasmic reticulum
B	0005788	cellular_component	endoplasmic reticulum lumen
B	0005794	cellular_component	Golgi apparatus
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
B	0005925	cellular_component	focal adhesion
B	0006826	biological_process	iron ion transport
B	0006879	biological_process	intracellular iron ion homeostasis
B	0006955	biological_process	immune response
B	0007608	biological_process	sensory perception of smell
B	0007611	biological_process	learning or memory
B	0009897	cellular_component	external side of plasma membrane
B	0009986	cellular_component	cell surface
B	0010977	biological_process	negative regulation of neuron projection development
B	0012507	cellular_component	ER to Golgi transport vesicle membrane
B	0016020	cellular_component	membrane
B	0019885	biological_process	antigen processing and presentation of endogenous peptide antigen via MHC class I
B	0019886	biological_process	antigen processing and presentation of exogenous peptide antigen via MHC class II
B	0023026	molecular_function	MHC class II protein complex binding
B	0030670	cellular_component	phagocytic vesicle membrane
B	0031901	cellular_component	early endosome membrane
B	0031902	cellular_component	late endosome membrane
B	0031905	cellular_component	early endosome lumen
B	0032092	biological_process	positive regulation of protein binding
B	0033077	biological_process	T cell differentiation in thymus
B	0034756	biological_process	regulation of iron ion transport
B	0035580	cellular_component	specific granule lumen
B	0042026	biological_process	protein refolding
B	0042605	molecular_function	peptide antigen binding
B	0042612	cellular_component	MHC class I protein complex
B	0042613	cellular_component	MHC class II protein complex
B	0042802	molecular_function	identical protein binding
B	0042803	molecular_function	protein homodimerization activity
B	0042824	cellular_component	MHC class I peptide loading complex
B	0045646	biological_process	regulation of erythrocyte differentiation
B	0048260	biological_process	positive regulation of receptor-mediated endocytosis
B	0050680	biological_process	negative regulation of epithelial cell proliferation
B	0050768	biological_process	negative regulation of neurogenesis
B	0050778	biological_process	positive regulation of immune response
B	0050870	biological_process	positive regulation of T cell activation
B	0051289	biological_process	protein homotetramerization
B	0055038	cellular_component	recycling endosome membrane
B	0060586	biological_process	multicellular organismal-level iron ion homeostasis
B	0070062	cellular_component	extracellular exosome
B	0071281	biological_process	cellular response to iron ion
B	0071283	biological_process	cellular response to iron(III) ion
B	0071316	biological_process	cellular response to nicotine
B	1900121	biological_process	negative regulation of receptor binding
B	1900122	biological_process	positive regulation of receptor binding
B	1904434	biological_process	positive regulation of ferrous iron binding
B	1904437	biological_process	positive regulation of transferrin receptor binding
B	1904724	cellular_component	tertiary granule lumen
B	1990000	biological_process	amyloid fibril formation
B	1990712	cellular_component	HFE-transferrin receptor complex
B	2000774	biological_process	positive regulation of cellular senescence
B	2000978	biological_process	negative regulation of forebrain neuron differentiation
E	0000139	cellular_component	Golgi membrane
E	0001913	biological_process	T cell mediated cytotoxicity
E	0001916	biological_process	positive regulation of T cell mediated cytotoxicity
E	0002237	biological_process	response to molecule of bacterial origin
E	0002376	biological_process	immune system process
E	0002474	biological_process	antigen processing and presentation of peptide antigen via MHC class I
E	0002481	biological_process	antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent
E	0002502	biological_process	peptide antigen assembly with MHC class I protein complex
E	0002503	biological_process	peptide antigen assembly with MHC class II protein complex
E	0002726	biological_process	positive regulation of T cell cytokine production
E	0005198	molecular_function	structural molecule activity
E	0005515	molecular_function	protein binding
E	0005576	cellular_component	extracellular region
E	0005615	cellular_component	extracellular space
E	0005765	cellular_component	lysosomal membrane
E	0005783	cellular_component	endoplasmic reticulum
E	0005788	cellular_component	endoplasmic reticulum lumen
E	0005794	cellular_component	Golgi apparatus
E	0005829	cellular_component	cytosol
E	0005886	cellular_component	plasma membrane
E	0005925	cellular_component	focal adhesion
E	0006826	biological_process	iron ion transport
E	0006879	biological_process	intracellular iron ion homeostasis
E	0006955	biological_process	immune response
E	0007608	biological_process	sensory perception of smell
E	0007611	biological_process	learning or memory
E	0009897	cellular_component	external side of plasma membrane
E	0009986	cellular_component	cell surface
E	0010977	biological_process	negative regulation of neuron projection development
E	0012507	cellular_component	ER to Golgi transport vesicle membrane
E	0016020	cellular_component	membrane
E	0019885	biological_process	antigen processing and presentation of endogenous peptide antigen via MHC class I
E	0019886	biological_process	antigen processing and presentation of exogenous peptide antigen via MHC class II
E	0023026	molecular_function	MHC class II protein complex binding
E	0030670	cellular_component	phagocytic vesicle membrane
E	0031901	cellular_component	early endosome membrane
E	0031902	cellular_component	late endosome membrane
E	0031905	cellular_component	early endosome lumen
E	0032092	biological_process	positive regulation of protein binding
E	0033077	biological_process	T cell differentiation in thymus
E	0034756	biological_process	regulation of iron ion transport
E	0035580	cellular_component	specific granule lumen
E	0042026	biological_process	protein refolding
E	0042605	molecular_function	peptide antigen binding
E	0042612	cellular_component	MHC class I protein complex
E	0042613	cellular_component	MHC class II protein complex
E	0042802	molecular_function	identical protein binding
E	0042803	molecular_function	protein homodimerization activity
E	0042824	cellular_component	MHC class I peptide loading complex
E	0045646	biological_process	regulation of erythrocyte differentiation
E	0048260	biological_process	positive regulation of receptor-mediated endocytosis
E	0050680	biological_process	negative regulation of epithelial cell proliferation
E	0050768	biological_process	negative regulation of neurogenesis
E	0050778	biological_process	positive regulation of immune response
E	0050870	biological_process	positive regulation of T cell activation
E	0051289	biological_process	protein homotetramerization
E	0055038	cellular_component	recycling endosome membrane
E	0060586	biological_process	multicellular organismal-level iron ion homeostasis
E	0070062	cellular_component	extracellular exosome
E	0071281	biological_process	cellular response to iron ion
E	0071283	biological_process	cellular response to iron(III) ion
E	0071316	biological_process	cellular response to nicotine
E	1900121	biological_process	negative regulation of receptor binding
E	1900122	biological_process	positive regulation of receptor binding
E	1904434	biological_process	positive regulation of ferrous iron binding
E	1904437	biological_process	positive regulation of transferrin receptor binding
E	1904724	cellular_component	tertiary granule lumen
E	1990000	biological_process	amyloid fibril formation
E	1990712	cellular_component	HFE-transferrin receptor complex
E	2000774	biological_process	positive regulation of cellular senescence
E	2000978	biological_process	negative regulation of forebrain neuron differentiation

Functional Information from PDB Data

site_id	AC1
Number of Residues	11
Details	binding site for residue GOL A 301

Chain	Residue
A	ARG44
D	EDO310
D	HOH414
A	GLU45
A	PRO57
A	TRP60
A	ASP61
A	THR64
A	HOH620
D	GLN72
D	ARG75

---

site_id	AC2
Number of Residues	8
Details	binding site for residue GOL A 302

Chain	Residue
A	ASN80
A	GLY83
A	TYR84
A	LYS146
D	GLU154
D	ARG157
D	ALA158
D	GLU161

---

site_id	AC3
Number of Residues	9
Details	binding site for residue EDO A 303

Chain	Residue
A	GLN70
A	SER97
A	TYR99
A	ASN114
A	TYR116
A	EDO306
A	HOH657
A	HOH625
C	GLN3

---

site_id	AC4
Number of Residues	2
Details	binding site for residue EDO A 304

Chain	Residue
A	ARG62
A	GLN65

---

site_id	AC5
Number of Residues	5
Details	binding site for residue EDO A 305

Chain	Residue
A	ARG62
A	HOH611
D	GLN144
D	ARG145
D	GLU148

---

site_id	AC6
Number of Residues	6
Details	binding site for residue EDO A 306

Chain	Residue
A	THR73
A	ASP74
A	SER77
A	EDO303
A	HOH657
C	ARG7

---

site_id	AC7
Number of Residues	7
Details	binding site for residue EDO A 307

Chain	Residue
A	GLN115
A	TYR116
A	ASP122
A	ILE124
A	ALA125
A	THR134
B	TRP60

---

site_id	AC8
Number of Residues	7
Details	binding site for residue SO4 A 308

Chain	Residue
A	ALA150
A	ARG151
A	HOH666
D	GLY83
D	TYR84
D	TYR85
D	ASN86

---

site_id	AC9
Number of Residues	5
Details	binding site for residue SO4 A 309

Chain	Residue
A	PHE8
A	TYR27
A	ASP29
A	ASP30
B	HOH202

---

site_id	AD1
Number of Residues	6
Details	binding site for residue EDO B 101

Chain	Residue
A	PHE8
A	MET98
A	GLN115
B	SER57
B	LYS58
B	HOH203

---

site_id	AD2
Number of Residues	9
Details	binding site for residue GOL D 301

Chain	Residue
A	PRO57
A	HOH621
D	SER38
D	LYS68
D	ALA71
D	GLN72
D	ARG75
D	HOH418
D	HOH415

---

site_id	AD3
Number of Residues	3
Details	binding site for residue EDO D 302

Chain	Residue
D	ARG62
D	GLN65
D	HOH422

---

site_id	AD4
Number of Residues	7
Details	binding site for residue EDO D 303

Chain	Residue
D	GLN70
D	TYR99
D	ASN114
D	TYR116
D	HOH436
D	HOH429
F	GLN3

---

site_id	AD5
Number of Residues	8
Details	binding site for residue EDO D 304

Chain	Residue
A	ASP61
D	ARG14
D	PRO20
D	ARG21
D	SER38
D	ASP39
D	ARG75
D	HOH476

---

site_id	AD6
Number of Residues	6
Details	binding site for residue EDO D 305

Chain	Residue
D	THR73
D	ASP74
D	SER77
D	LEU95
D	HOH436
F	ARG7

---

site_id	AD7
Number of Residues	4
Details	binding site for residue EDO D 306

Chain	Residue
D	TYR27
D	ASP29
D	ASP30
D	HOH443

---

site_id	AD8
Number of Residues	4
Details	binding site for residue EDO D 307

Chain	Residue
D	ASP122
D	ALA125
D	THR134
D	HOH410

---

site_id	AD9
Number of Residues	6
Details	binding site for residue EDO D 308

Chain	Residue
A	LYS68
D	SER13
D	GLU19
D	HOH510
D	HOH445
D	HOH411

---

site_id	AE1
Number of Residues	6
Details	binding site for residue EDO D 309

Chain	Residue
A	GLY83
A	TYR84
A	ASN86
D	ALA150
D	ARG151
F	ARG7

---

site_id	AE2
Number of Residues	6
Details	binding site for residue EDO D 310

Chain	Residue
A	GOL301
D	GLU19
D	PRO20
D	ARG79
D	HOH407
D	HOH484

---

site_id	AE3
Number of Residues	6
Details	binding site for residue EDO E 101

Chain	Residue
D	VAL12
D	SER92
E	PRO32
E	SER33
E	ASP34
E	HOH212

---

site_id	AE4
Number of Residues	4
Details	binding site for residue EDO E 102

Chain	Residue
D	ARG21
E	SER33
E	ASP34
E	HOH215

---

site_id	AE5
Number of Residues	4
Details	binding site for residue EDO F 101

Chain	Residue
D	GLU55
D	GLU58
D	TYR59
F	ARG1

---

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	TYR257-HIS263
B	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
B	GLN2
D	SER143
D	LYS146
D	VAL152
D	TYR159
D	TYR171
E	GLN2
A	SER143
A	LYS146
A	VAL152
A	TYR159
A	TYR171
D	ASN63
D	TYR84

---

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
B	ILE1
E	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
B	LYS19
E	LYS58
E	LYS91
E	LYS94
B	LYS41
B	LYS48
B	LYS58
B	LYS91
B	LYS94
E	LYS19
E	LYS41
E	LYS48

---