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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN INTERLEUKIN-34 BOUND TO FAB1.1

Authors :   X. Ma, Y. Chen, S. Stawicki, Y. Wu, J. F. Bazan, M. A. Starovasnik

Date :   03 Feb 12 (Deposition) - 11 Apr 12 (Release) - 25 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B,H,I,L,M
Biol. Unit 1: A,B,H,I,L,M  (1x)
Biol. Unit 2: A (1x),B (1x),H (1x),I (1x),L (1x),M (1x)

Keywords :   Dimeric Four-Helix Bundle Cytokine, Igg, Glycosylation, Cytokine- Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Ma, W. Y. Lin, Y. Chen, S. Stawicki, K. Mukhyala, Y. Wu, F. Martin, J. F. Bazan, M. A. Starovasnik
Structural Basis For The Dual Recognition Of Helical Cytokines Il-34 And Csf-1 By Csf-1R.
Structure V. 20 676 2012
PubMed-ID: 22483114 | Reference-DOI: 10.1016/J.STR.2012.02.010

Molecule 1 - INTERLEUKIN-34
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	TNI PRO
	Expression System Taxid	:	7111
	Fragment	:	ACTIVE CORE
	Gene	:	IL34, C16ORF77
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	IL-34

Molecule 2 - FAB1.1 HEAVY CHAIN
	Chains	:	H, I
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Taxid	:	10029
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	PROTEIN SELECTED BY PHAGE DISPLAY

Molecule 3 - FAB1.1 LIGHT CHAIN
	Chains	:	L, M
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Taxid	:	10029
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	PROTEIN SELECTED BY PHAGE DISPLAY

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	H	I	L	M
Biological Unit 1 (1x)	:	A	B	H	I	L	M
Biological Unit 2 (1x)	:	A (1x)	B (1x)	H (1x)	I (1x)	L (1x)	M (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (3, 9)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:69 , VAL A:71 , ASN A:76 , ARG A:79 , NAG A:302	BINDING SITE FOR RESIDUE NAG A 301
2	AC2	SOFTWARE	TYR A:68 , GLU A:69 , LYS A:157 , NAG A:301 , MAN A:303	BINDING SITE FOR RESIDUE NAG A 302
3	AC3	SOFTWARE	TYR A:68 , NAG A:302 , BMA A:304 , MAN A:305	BINDING SITE FOR RESIDUE MAN A 303
4	AC4	SOFTWARE	MAN A:303	BINDING SITE FOR RESIDUE BMA A 304
5	AC5	SOFTWARE	MAN A:303 , GLN H:13	BINDING SITE FOR RESIDUE MAN A 305
6	AC6	SOFTWARE	TYR B:68 , GLU B:69 , VAL B:71 , PHE B:72 , ASN B:76 , ARG B:79 , NAG B:302	BINDING SITE FOR RESIDUE NAG B 301
7	AC7	SOFTWARE	TYR B:68 , GLU B:69 , LYS B:157 , NAG B:301 , MAN B:303	BINDING SITE FOR RESIDUE NAG B 302
8	AC8	SOFTWARE	NAG B:302 , BMA B:304	BINDING SITE FOR RESIDUE MAN B 303
9	AC9	SOFTWARE	MAN B:303	BINDING SITE FOR RESIDUE BMA B 304

Asymmetric Unit

No.	Residues
1	A:35	-	A:180
2	A:177	-	A:191
3	B:35	-	B:180
4	H:22	-	H:92
5	H:140	-	H:196
6	H:216	-	L:214
7	I:22	-	I:92
8	I:140	-	I:196
9	L:23	-	L:88
10	L:134	-	L:194
11	M:23	-	M:88
12	M:134	-	M:194

Asymmetric Unit

No.	Residues
1	Phe H:146	-	Pro H:147
2	Glu H:148	-	Pro H:149
3	Ser L:7	-	Pro L:8
4	Phe L:94	-	Pro L:95
5	Tyr L:140	-	Pro L:141
6	Phe I:146	-	Pro I:147
7	Glu I:148	-	Pro I:149
8	Ser M:7	-	Pro M:8
9	Phe M:94	-	Pro M:95
10	Tyr M:140	-	Pro M:141

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_033164	E	123	Q	IL34_HUMAN	Polymorphism	8046424	A/B	E	123	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_033164	E	123	Q	IL34_HUMAN	Polymorphism	8046424	A/B	E	123	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_033164	E	123	Q	IL34_HUMAN	Polymorphism	8046424	A/B	E	123	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 4DKE)

(no "Exon" information available for 4DKE)

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:157
 aligned with IL34_HUMAN | Q6ZMJ4 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:159
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183         
          IL34_HUMAN     34 ECTVTGFLRDKLQYRSRLQYMKHYFPINYKISVPYEGVFRIANVTRLQRAQVSERELRYLWVLVSLSATESVQDVLLEGHPSWKYLQEVETLLLNVQQGLTDVEVSPKVESVLSLLNAPGPNLKLVRPKALLDNCFRVMELLYCSCCKQSSVLNWQDCE  192
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh........eeehhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..--.eeehhhhhhhhhhhhhhhhhh.......hhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------Q--------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4dke A   34 ECTVTGFLRDKLQYRSRLQYMKHYFPINYKISVPYEGVFRIANVTRLQRAQVSERELRYLWVLVSLSATESVQDVLLEGHPSWKYLQEVETLLLNVQQGLTDVEVSPKVESVLSLLNAPG--LKLVRPKALLDNCFRVMELLYCSCCKQSSVLNWQDCE  192
                                    43        53        63        73        83        93       103       113       123       133       143       153  |    163       173       183         
                                                                                                                                                 153  |                                    
                                                                                                                                                    156

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with IL34_HUMAN | Q6ZMJ4 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:148
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172        
          IL34_HUMAN     33 EECTVTGFLRDKLQYRSRLQYMKHYFPINYKISVPYEGVFRIANVTRLQRAQVSERELRYLWVLVSLSATESVQDVLLEGHPSWKYLQEVETLLLNVQQGLTDVEVSPKVESVLSLLNAPGPNLKLVRPKALLDNCFRVMELLYCSCC  180
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh........eeehhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..--------..hhhhhh..---..eeehhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------Q--------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4dke B   33 EECTVTGFLRDKLQYRSRLQYMKHYFPINYKISVPYEGVFRIANVTRLQRAQVSERELRYLWVLVSLSATESVQDVLLEGHPSWKYLQEVETLLLNVQQGL--------VESVLSLLNA---NLKLVRPKALLDNCFRVMELLYCSCC  180
                                    42        52        62        72        82        92       102       112       122       132|      142        |-  |    162       172        
                                                                                                                              133      142      151 155

Chain H from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee........eeeeee.....eeeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeeee..hhhhhh.eeee...eeeee........eeeee.....eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4dke H    1 EVQLVESGGGLVQPGGSLRLSCAASGFTFSSTWIHWVRQAPGKGLEWVARISPYYYYSDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARGLGKGSKRGAMDYWGQGTLVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111       121      |136       146       156       166       176       186       196       206       216
                                                                              52A                            82A||               100A||||                         128|                                                                                  
                                                                                                              82B|                100B|||                          134                                                                                  
                                                                                                               82C                 100C||                                                                                                               
                                                                                                                                    100D|                                                                                                               
                                                                                                                                     100E

Chain I from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee........eeeeee.....eeeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeeee.........eeee...eeeee........eeeee....eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee..........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4dke I    1 EVQLVESGGGLVQPGGSLRLSCAASGFTFSSTWIHWVRQAPGKGLEWVARISPYYYYSDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARGLGKGSKRGAMDYWGQGTLVTVSSASTKGPSVFPLAPSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111       121     ||138       148       158       168       178       188       198       208      
                                                                              52A                            82A||               100A||||                        127|                                                                               
                                                                                                              82B|                100B|||                         135                                                                               
                                                                                                               82C                 100C||                                                                                                           
                                                                                                                                    100D|                                                                                                           
                                                                                                                                     100E

Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4dke L    1 DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSFYFPNTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain M from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee........eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4dke M    1 DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSFYFPNTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 4DKE)

(no "CATH Domain" information available for 4DKE)

(no "Pfam Domain" information available for 4DKE)

Asymmetric Unit(hide GO term definitions)

Chain A,B (IL34_HUMAN | Q6ZMJ4)

molecular function
	GO:0005125	cytokine activity	Functions to control the survival, growth, differentiation and effector function of tissues and cells.
	GO:0008083	growth factor activity	The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
	GO:0005157	macrophage colony-stimulating factor receptor binding	Interacting selectively and non-covalently with the macrophage colony-stimulating factor receptor.
biological process
	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.
	GO:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0045651	positive regulation of macrophage differentiation	Any process that activates or increases the frequency, rate or extent of macrophage differentiation.
	GO:0045657	positive regulation of monocyte differentiation	Any process that activates or increases the frequency, rate or extent of monocyte differentiation.
	GO:0001934	positive regulation of protein phosphorylation	Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Glu H:148 - Pro H:149	[ RasMol ]
		Glu I:148 - Pro I:149	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Phe I:146 - Pro I:147	[ RasMol ]
		Phe L:94 - Pro L:95	[ RasMol ]
		Phe M:94 - Pro M:95	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Ser M:7 - Pro M:8	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Tyr M:140 - Pro M:141	[ RasMol ]

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	4dke
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	IL34_HUMAN \| Q6ZMJ4	:	4dkc 4dkd 4dkf

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (12, 12)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

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