3V52 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE OF A MONOCLONAL ANTIBODY COMPLEXED WITH ITS MHC-I ANTIGEN

Authors :   M. G. Mage, M. A. Dolan, R. Wang, L. F. Boyd, M. J. Revilleza, H. Robinson, K. Natarajan, N. B. Myers, T. H. Hansen, D. H. Margulies

Date :   15 Dec 11 (Deposition) - 25 Jul 12 (Release) - 01 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : H,L,P

Keywords :   Ig Domain, 3-10 Helix, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. G. Mage, M. A. Dolan, R. Wang, L. F. Boyd, M. J. Revilleza, H. Robinson K. Natarajan, N. B. Myers, T. H. Hansen, D. H. Margulies
The Peptide-Receptive Transition State Of Mhc Class I Molecules: Insight From Structure And Molecular Dynamics.
J. Immunol. V. 189 1391 2012
PubMed-ID: 22753930 | Reference-DOI: 10.4049/JIMMUNOL.1200831

Molecule 1 - ANTI-MHC-I MONOCLONAL ANTIBODY, 64-3-7 H CHAIN
	Chains	:	H
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - ANTI-MHC-I MONOCLONAL ANTIBODY, 64-3-7 L CHAIN
	Chains	:	L
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, L-D ALPHA CHAIN
	Chains	:	P
	Engineered	:	YES
	Fragment	:	H-2LD PEPTIDE P46-53
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	SYNTHETIC PEPTIDE
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	H	L	P

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN H:101 , ASN L:35 , TYR L:37 , LYS L:55 , PRO P:47 , PRO P:50	BINDING SITE FOR RESIDUE EDO L 301

Asymmetric/Biological Unit

No.	Residues
1	H:22	-	H:96
2	H:132	-	L:218
3	H:144	-	H:199
4	L:23	-	L:93
5	L:138	-	L:198

Asymmetric/Biological Unit

No.	Residues
1	Glu H:42	-	Lys H:43
2	Phe H:150	-	Pro H:151
3	Glu H:152	-	Ser H:153
4	Trp H:192	-	Pro H:193
5	Thr L:7	-	Pro L:8
6	Tyr L:144	-	Pro L:145

(no "SAP(SNP)/Variant" information available for 3V52)

(no "PROSITE Motif" information available for 3V52)

(no "Exon" information available for 3V52)

Asymmetric/Biological 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 H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee.....eeeeeee...hhhhheeeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..eeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v52 H   2 VKLVESEGGLVQPGSSMKLSCTASGFTFSDYYMAWVRQVPEKGLEWVANINYDGSSTYYLDSLKGRFIISRDIAKNILYLQMSSLRCEDTATYYCARLTNGYLDVWGAGTTVTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLESGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEP 216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain L from PDB  Type:PROTEIN  Length:218
 aligned with A2NHM3_MOUSE | A2NHM3 from UniProtKB/TrEMBL  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
         A2NHM3_MOUSE     1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 219
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....-ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v52 L   1 DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPNLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVP-TFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 218
                                    10        20        30        40        50        60        70        80        90       100 |     109       119       129       139       149       159       169       179       189       199       209         
                                                                                                                             100 |                                                                                                                     
                                                                                                                               101

Chain P from PDB  Type:PROTEIN  Length:8
 aligned with HA1L_MOUSE | P01897 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:8
           HA1L_MOUSE    70 EPQAPWME  77
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ...hhhhh Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 3v52 P  46 EPQAPWME  53

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 '\|'

(no "SCOP Domain" information available for 3V52)

(no "CATH Domain" information available for 3V52)

(no "Pfam Domain" information available for 3V52)

Asymmetric/Biological Unit(hide GO term definitions)

Chain L (A2NHM3_MOUSE | A2NHM3)

Chain P (HA1L_MOUSE | P01897)

molecular function
	GO:0042605	peptide antigen binding	Interacting selectively and non-covalently with an antigen peptide.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
	GO:0019882	antigen processing and presentation	The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
	GO:0002479	antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class I molecule. Class I here refers to classical class I molecules.
	GO:0002474	antigen processing and presentation of peptide antigen via MHC class I	The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules.
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
cellular component
	GO:0042612	MHC class I protein complex	A transmembrane protein complex composed of a MHC class I alpha chain and an invariant beta2-microglobin chain, and with or without a bound peptide antigen. Class I here refers to classical class I molecules.
	GO:0071556	integral component of lumenal side of endoplasmic reticulum membrane	The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the lumenal side of the membrane.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0030670	phagocytic vesicle membrane	The lipid bilayer surrounding a phagocytic vesicle.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu H:152 - Ser H:153	[ RasMol ]
		Glu H:42 - Lys H:43	[ RasMol ]
		Phe H:150 - Pro H:151	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Trp H:192 - Pro H:193	[ RasMol ]
		Tyr L:144 - Pro L:145	[ RasMol ]

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3uo1	STRUCTURE OF A MONOCLONAL ANTIBODY COMPLEXED WITH ITS MHC-I ANTIGEN
3uyr	STRUCTURE OF A MONOCLONAL ANTIBODY COMPLEXED WITH ITS MHC-I ANTIGEN
3v4u	STRUCTURE OF A MONOCLONAL ANTIBODY COMPLEXED WITH ITS MHC-I ANTIGEN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (5, 5)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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