1RYX - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HEN SERUM TRANSFERRIN IN APO- FORM

Authors :   J. K. Dattagupta, P. G. Thakurta, D. Choudhury, R. Dasgupta

Date :   23 Dec 03 (Deposition) - 13 Jul 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.50

Chains :   Asym./Biol. Unit : A

Keywords :   Hen Serum Transferrin, Apo- Form, Domain Orientation, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. G. Thakurta, D. Choudhury, R. Dasgupta, J. K. Dattagupta
Tertiary Structural Changes Associated With Iron Binding And Release In Hen Serum Transferrin: A Crystallographic And Spectroscopic Study
Biochem. Biophys. Res. Commun. V. 316 1124 2004
PubMed-ID: 15044101 | Reference-DOI: 10.1016/J.BBRC.2004.02.165
(for further references see the PDB file header)

Molecule 1 - OVOTRANSFERRIN
	Chains	:	A
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Synonym	:	CONALBUMIN, ALLERGEN GAL D 3, GAL D III, SERUM TRANSFERRIN
	Tissue	:	HEN SERUM

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1RYX)

(no "Site" information available for 1RYX)

Asymmetric/Biological Unit

No.	Residues
1	A:10	-	A:45
2	A:20	-	A:36
3	A:115	-	A:197
4	A:160	-	A:174
5	A:171	-	A:182
6	A:228	-	A:242
7	A:348	-	A:380
8	A:358	-	A:371
9	A:405	-	A:680
10	A:421	-	A:643
11	A:454	-	A:530
12	A:478	-	A:671
13	A:488	-	A:502
14	A:499	-	A:513
15	A:570	-	A:584

(no "Cis Peptide Bond" information available for 1RYX)

Asymmetric/Biological Unit (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRFE_CHICK_001 *	A	83	V	TRFE_CHICK	---	---	A	A	64	V
2	UniProt	VAR_TRFE_CHICK_002 *	V	100	I	TRFE_CHICK	---	---	A	V	81	I
3	UniProt	VAR_TRFE_CHICK_003 *	R	154	W	TRFE_CHICK	---	---	A	R	135	W
4	UniProt	VAR_TRFE_CHICK_004 *	S	686	N	TRFE_CHICK	---	---	A	S	667	N
	* ID not provided by source

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

Asymmetric/Biological Unit (4, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRANSFERRIN_LIKE_4	PS51408	Transferrin-like domain profile.	TRFE_CHICK	26-352 364-689	2	A:7-333 A:345-670
2	TRANSFERRIN_LIKE_1	PS00205	Transferrin-like domain signature 1.	TRFE_CHICK	111-120 450-459	2	A:92-101 A:431-440
3	TRANSFERRIN_LIKE_2	PS00206	Transferrin-like domain signature 2.	TRFE_CHICK	210-226 543-558	2	A:191-207 A:524-539
4	TRANSFERRIN_LIKE_3	PS00207	Transferrin-like domain signature 3.	TRFE_CHICK	242-272 584-614	2	A:223-253 A:565-595

(no "Exon" information available for 1RYX)

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 A from PDB  Type:PROTEIN  Length:686
 aligned with TRFE_CHICK | P02789 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:686
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699      
           TRFE_CHICK    20 APPKSVIRWCTISSPEEKKCNNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAISLDGGQAFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAVAVVKKGTEFTVNDLQGKTSCHTGLGRSAGWNIPIGTLLHRGAIEWEGIESGSVEQAVAKFFSASCVPGATIEQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYELLCLDGSRQPVDNYKTCNWARVAAHAVVARDDNKVEDIWSFLSKAQSDFGVDTKSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPSLMDSQLYLGFEYYSAIQSMRKDQLTPSPRENRIQWCAVGKDEKSKCDRWSVVSNGDVECTVVDETKDCIIKIMKGEADAVALDGGLVYTAGVCGLVPVMAERYDDESQCSKTDERPASYFAVAVARKDSNVNWNNLKGKKSCHTAVGRTAGWVIPMGLIHNRTGTCNFDEYFSEGCAPGSPPNSRLCQLCQGSGGIPPEKCVASSHEKYFGYTGALRCLVEKGDVAFIQHSTVEENTGGKNKADWAKNLQMDDFELLCTDGRRANVMDYRECNLAEVPTHAVVVRPEKANKIRDLLERQEKRFGVNGSEKSKFMMFESQNKDLLFKDLTKCLFKVREGTTYKEFLGDKFYTVISSLKTCNPSDILQMCSFLEGK 705
               SCOP domains d1ryxa1 A:1-334 Ovotransferrin                                                                                                                                                                                                                                                                                                                d1ryxa2 A:335-686 Ovotransferrin                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ----1ryxA01 A:5-91,A:248-339 Periplasmic binding protein-like II                           1ryxA02 A:92-247 Periplasmic binding protein-like II                                                                                                        1ryxA01 A:5-91,A:248-339 Periplasmic binding protein-like II                                1ryxA03 A:340-430,A:590-685 Periplasmic binding protein-like II                            1ryxA04 A:431-589 Periplasmic binding protein-like II                                                                                                          1ryxA03 A:340-430,A:590-685 Periplasmic binding protein-like II                                 - CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Transferrin-1ryxA01 A:345-670                                                                                                                                                                                                                                                                                                         ---------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Transferrin-1ryxA02 A:345-670                                                                                                                                                                                                                                                                                                         ---------------- Pfam domains (2)
         Sec.struct. author .............hhhhhhh..hhhhhhh...........hhhhhhhhhhh....ee..hhhhhhhhh......eeeeeee...........ee..............................hhhhhhhhhhhh.....hhhhhhhhhhhhh....................................hhhhhhhhh............hhhhhh...........................ee....eeee.....hhhhhhhhhhhhhhhh..............................ee.............hhhhhhhhhhh..............................................hhhhhhhhhh....eee..hhhhhhhhhh..........................eeeeee.....hhhhh....ee.....hhhhh.hhhhhhhhh....hhhhh...ee.................................hhhhhhhhhhh......eee..hhhhhh............hhh.eee..........hhhhhh........eee.........hhhhhh........hhhhhh...........................hhhhhhh.hhhhhhhhh.....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------V----------------I-----------------------------------------------------W---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N------------------- SAPs(SNPs)
                PROSITE (1) ------TRANSFERRIN_LIKE_4  PDB: A:7-333 UniProt: 26-352                                                                                                                                                                                                                                                                                       -----------TRANSFERRIN_LIKE_4  PDB: A:345-670 UniProt: 364-689                                                                                                                                                                                                                                                                                   ---------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------TRANSFERRI-----------------------------------------------------------------------------------------TRANSFERRIN_LIKE_---------------TRANSFERRIN_LIKE_3             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSFERRI-----------------------------------------------------------------------------------TRANSFERRIN_LIKE-------------------------TRANSFERRIN_LIKE_3             ------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ryx A   1 APPKSVIRWCTISSPEEKKCNNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAISLDGGQAFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAVAVVKKGTEFTVNDLQGKTSCHTGLGRSAGWNIPIGTLLHRGAIEWEGIESGSVEQAVAKFFSASCVPGATIEQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYELLCLDGSRQPVDNYKTCNWARVAAHAVVARDDNKVEDIWSFLSKAQSDFGVDTKSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPSLMDSQLYLGFEYYSAIQSMRKDQLTPSPRENRIQWCAVGKDEKSKCDRWSVVSNGDVECTVVDETKDCIIKIMKGEADAVALDGGLVYTAGVCGLVPVMAERYDDESQCSKTDERPASYFAVAVARKDSNVNWNNLKGKKSCHTAVGRTAGWVIPMGLIHNRTGTCNFDEYFSEGCAPGSPPNSRLCQLCQGSGGIPPEKCVASSHEKYFGYTGALRCLVEKGDVAFIQHSTVEENTGGKNKADWAKNLQMDDFELLCTDGRRANVMDYRECNLAEVPTHAVVVRPEKANKIRDLLERQEKRFGVNGSEKSKFMMFESQNKDLLFKDLTKCLFKVREGTTYKEFLGDKFYTVISSLKTCNPSDILQMCSFLEGK 686
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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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: Transferrin (82)

Protein domain: Ovotransferrin (14)

Chicken (Gallus gallus) [TaxId: 9031] (9)

1a	d1ryxa1	A:1-334
1b	d1ryxa2	A:335-686

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: D-Maltodextrin-Binding Protein; domain 2 (600)

Homologous Superfamily: Periplasmic binding protein-like II (486)

Chicken (Gallus gallus) (10)

1a	1ryxA02	A:92-247
1b	1ryxA04	A:431-589
1c	1ryxA01	A:5-91,A:248-339
1d	1ryxA03	A:340-430,A:590-685

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PBP (391)

Family: Transferrin (53)

Gallus gallus (Chicken) (7)

1a	Transferrin-1ryxA01	A:345-670
1b	Transferrin-1ryxA02	A:345-670

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TRFE_CHICK | P02789)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006953	acute-phase response	An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	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/Biological Unit
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	Cis Peptide Bonds
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	TRFE_CHICK \| P02789	:	1aiv 1d9k 1iej 1iq7 1jl4 1n04 1nft 1nnt 1ovt 1tfa 2d3i

1n04	DIFERRIC CHICKEN SERUM TRANSFERRIN AT 2.8 A RESOLUTION.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (15, 15)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

PROSITE Motifs (4, 8)

Exons (0, 0)

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