2RIV - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE REACTIVE LOOP CLEAVED HUMAN THYROXINE BINDING GLOBULIN

Authors :   A. Zhou, Z. Wei, P. L. D. Stanley, R. J. Read, P. E. Stein, R. W. Carrell

Date :   12 Oct 07 (Deposition) - 14 Oct 08 (Release) - 16 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Tbg, Serpin, Cleaved, Thyroxine Binding Globulin, Thyroxine, Disease Mutation, Glycoprotein, Secreted, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Qi, F. Loiseau, W. L. Chan, Y. Yan, Z. Wei, L. G. Milroy, R. M. Myers, S. V. Ley, R. J. Read, R. W. Carrell, A. Zhou
Allosteric Modulation Of Hormone Release From Thyroxine And Corticosteroid-Binding Globulins
J. Biol. Chem. V. 286 16163 2011
PubMed-ID: 21325280 | Reference-DOI: 10.1074/JBC.M110.171082

Molecule 1 - THYROXINE-BINDING GLOBULIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21 STAR (DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN, UNP RESIDUES 33-375
	Gene	:	SERPINA7, TBG
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TBG, T4-BINDING GLOBULIN, SERPIN A7

Molecule 2 - THYROXINE-BINDING GLOBULIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21 STAR (DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	REACTIVE LOOP CLEAVED TBG, C-TEEMINGLY DOMAIN, UNP RESIDUES 376-415
	Gene	:	SERPINA7, TBG
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TBG, T4-BINDING GLOBULIN, SERPIN A7

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 5)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:287 , HIS A:336 , GLY A:338 , GLU A:339 , LYS A:340 , GLY A:341 , HOH A:414 , HOH A:416 , HOH A:448 , HOH A:514	BINDING SITE FOR RESIDUE SO4 A 1
2	AC2	SOFTWARE	SER A:242 , LYS A:243 , ASN A:244 , HOH A:445 , ARG B:378	BINDING SITE FOR RESIDUE SO4 A 2
3	AC3	SOFTWARE	PHE A:62 , GLN A:69 , GLN A:89 , LYS A:125 , THR A:210 , THR A:211 , THR A:212 , HOH A:606	BINDING SITE FOR RESIDUE GOL A 356
4	AC4	SOFTWARE	SER A:197 , THR A:199 , GLU A:200 , ASP A:201 , HOH A:717	BINDING SITE FOR RESIDUE GOL A 357
5	AC5	SOFTWARE	GLN A:238 , ASN A:273 , HOH A:404 , HOH A:629 , ARG B:378	BINDING SITE FOR RESIDUE GOL A 358

(no "SS Bond" information available for 2RIV)

(no "Cis Peptide Bond" information available for 2RIV)

Asymmetric Unit (9, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_007102	S	43	T	THBG_HUMAN	Polymorphism	72554662	A	S	23	T
2	UniProt	VAR_007103	I	116	N	THBG_HUMAN	Polymorphism	28933689	A	I	96	N
3	UniProt	VAR_007104	A	133	P	THBG_HUMAN	Polymorphism	28933688	A	A	113	P
4	UniProt	VAR_007105	D	191	N	THBG_HUMAN	Polymorphism	1050086	A	D	171	N
5	UniProt	VAR_007106	A	211	T	THBG_HUMAN	Polymorphism	2234036	A	A	191	T
6	UniProt	VAR_007107	L	247	P	THBG_HUMAN	Polymorphism	28937312	A	L	227	P
7	UniProt	VAR_007108	L	303	F	THBG_HUMAN	Polymorphism	1804495	A	L	283	F
8	UniProt	VAR_007109	H	351	Y	THBG_HUMAN	Polymorphism	72554659	A	H	331	Y
9	UniProt	VAR_007110	P	383	L	THBG_HUMAN	Polymorphism	72554658	A B	A	352 363	L

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

Biological Unit 1 (9, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_007102	S	43	T	THBG_HUMAN	Polymorphism	72554662	A	S	23	T
2	UniProt	VAR_007103	I	116	N	THBG_HUMAN	Polymorphism	28933689	A	I	96	N
3	UniProt	VAR_007104	A	133	P	THBG_HUMAN	Polymorphism	28933688	A	A	113	P
4	UniProt	VAR_007105	D	191	N	THBG_HUMAN	Polymorphism	1050086	A	D	171	N
5	UniProt	VAR_007106	A	211	T	THBG_HUMAN	Polymorphism	2234036	A	A	191	T
6	UniProt	VAR_007107	L	247	P	THBG_HUMAN	Polymorphism	28937312	A	L	227	P
7	UniProt	VAR_007108	L	303	F	THBG_HUMAN	Polymorphism	1804495	A	L	283	F
8	UniProt	VAR_007109	H	351	Y	THBG_HUMAN	Polymorphism	72554659	A	H	331	Y
9	UniProt	VAR_007110	P	383	L	THBG_HUMAN	Polymorphism	72554658	A A	A	352 363	L

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
9	UniProt	VAR_007110	P	383	L	THBG_HUMAN	Polymorphism	72554658	A B	A	352 363	L

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

Biological Unit 3 (9, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_007102	S	43	T	THBG_HUMAN	Polymorphism	72554662	A	S	23	T
2	UniProt	VAR_007103	I	116	N	THBG_HUMAN	Polymorphism	28933689	A	I	96	N
3	UniProt	VAR_007104	A	133	P	THBG_HUMAN	Polymorphism	28933688	A	A	113	P
4	UniProt	VAR_007105	D	191	N	THBG_HUMAN	Polymorphism	1050086	A	D	171	N
5	UniProt	VAR_007106	A	211	T	THBG_HUMAN	Polymorphism	2234036	A	A	191	T
6	UniProt	VAR_007107	L	247	P	THBG_HUMAN	Polymorphism	28937312	A	L	227	P
7	UniProt	VAR_007108	L	303	F	THBG_HUMAN	Polymorphism	1804495	A	L	283	F
8	UniProt	VAR_007109	H	351	Y	THBG_HUMAN	Polymorphism	72554659	A	H	331	Y
9	UniProt	VAR_007110	P	383	L	THBG_HUMAN	Polymorphism	72554658	A A/B	A	352 363	L

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	THBG_HUMAN	385-395	1	B:365-375

Biological Unit 1 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	THBG_HUMAN	385-395	0	-

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	THBG_HUMAN	385-395	1	B:365-375

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	THBG_HUMAN	385-395	1	B:365-375

Asymmetric Unit (4, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000372563	1	ENSE00001458103	X:105282729-105282689	41	THBG_HUMAN	-	0	0	-	-
1.2b	ENST00000372563	2b	ENSE00001458102	X:105281066-105280428	639	THBG_HUMAN	1-208	208	1	A:17-188 -	172 -
1.3a	ENST00000372563	3a	ENSE00000840356	X:105279376-105279103	274	THBG_HUMAN	208-299	92	1	A:188-279 -	92 -
1.4	ENST00000372563	4	ENSE00000840355	X:105278373-105278226	148	THBG_HUMAN	299-348	50	1	A:279-328 -	50 -
1.5b	ENST00000372563	5b	ENSE00000840354	X:105277694-105277197	498	THBG_HUMAN	349-415	67	2	A:329-355 (gaps) B:362-395	38 34

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:339
 aligned with THBG_HUMAN | P05543 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:350
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386
           THBG_HUMAN    37 ATLYKMSSINADFAFNLYRRFTVETPDKNIFFSPVSISAALVMLSFGACCSTQTEIVETLGFNLTDTPMVEIQHGFQHLICSLNFPKKELELQIGNALFIGKHLKPLAKFLNDVKTLYETEVFSTDFSNISAAKQEINSHVEMQTKGKVVGLIQDLKPNTIMVLVNYIHFKAQWANPFDPSKTEDSSSFLIDKTTTVQVPMMHQMEQYYHLVDMELNCTVLQMDYSKNALALFVLPKEGQMESVEAAMSSKTLKKWNRLLQKGWVDLFVPKFSISATYDLGATLLKMGIQHAYSENADFSGLTEDNGLKLSNAAHKAVLHIGEKGTEAAAVPEVELSDQPENTFLHPIIQ 386
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2rivA01 A:17-190,A:287-355 Antithrombin, subunit I, domain 2                                                                                                                  2rivA02 A:191-286 Alpha-1-antitrypsin, domain 1                                                 2rivA01 A:17-190,A:287-355 Antithrombin, subunit I, domain 2                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.....hhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh................eeeeeeeeeeee.....hhhhheeeeeeeee..eeeeeeeeeeeeeeeeeee....eeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhheeeeeeeeee.eeeeeeeehhhhhhhhh.hhhhh.............eeeeeeeeeeeeee...eeeeeee-----------eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------T------------------------------------------------------------------------N----------------P---------------------------------------------------------N-------------------T-----------------------------------P-------------------------------------------------------F-----------------------------------------------Y----------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SE PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:17-188 UniProt: 1-208 [INCOMPLETE]                                                                                                                        ------------------------------------------------------------------------------------------Exon 1.4  PDB: A:279-328 UniProt: 299-348         Exon 1.5b  PDB: A:329-355 (gaps)       Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.3a  PDB: A:188-279 UniProt: 208-299                                                  --------------------------------------------------------------------------------------- Transcript 1 (2)
                 2riv A  17 ATLYKMSSINADFAFNLYRRFTVETPDKNIFFSPVSISAALVMLSFGACCSTQTEIVETLGFNLTDTPMVEIQHGFQHLICSLNFPKKELELQIGNALFIGKHLKPLAKFLNDVKTLYETEVFSTDFSNISAAKQEINSHVEMQTKGKVVGLIQDLKPNTIMVLVNYIHFKAQWANPFDPSKTEDSSSFLIDKTTTVQVPMMHQMEQYYHLVDMELNCTVLQMDYSKNALALFVLPKEGQMESVEAAMSSKTLKKWNRLLQKGWVDLFVPKFSISATYDLGATLLKMGIQHAYSENADFSGLTEDNGLKLSNAAHKAVLHIGEKGTEAAGA-----------MFLEAIPR 355
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346|        -  |    355
                                                                                                                                                                                                                                                                                                                                                                    347         348

Chain B from PDB  Type:PROTEIN  Length:34
 aligned with THBG_HUMAN | P05543 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:34
                                   391       401       411    
           THBG_HUMAN   382 HPIIQIDRSFMLLILERSTRSILFLGKVVNPTEA 415
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
           Pfam domains (1) Serpin-2rivB01 B:362-392       --- Pfam domains (1)
           Pfam domains (2) Serpin-2rivB02 B:362-392       --- Pfam domains (2)
         Sec.struct. author ..eee....eeeeeee....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---SERPIN     -------------------- PROSITE
           Transcript 1 (1) Exon 1.5b  PDB: B:362-395          Transcript 1 (1)
           Transcript 1 (2) ---------------------------------- Transcript 1 (2)
                 2riv B 362 HPIIQIDRSFMLLILERSTRSILFLGKVVNPTEA 395
                                   371       381       391

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 2RIV)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Antithrombin; Chain I, domain 2 (100)

Homologous Superfamily: Antithrombin, subunit I, domain 2 (100)

Human (Homo sapiens) (80)

2rivA01

A:17-190,A:287-355

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Alpha-1-antitrypsin; domain 1 (101)

Homologous Superfamily: Alpha-1-antitrypsin, domain 1 (101)

Human (Homo sapiens) (81)

2rivA02

A:191-286

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Serpin] (63)

Family: Serpin (63)

Homo sapiens (Human) (41)

1a	Serpin-2rivB01	B:362-392
1b	Serpin-2rivB02	B:362-392

Asymmetric Unit(hide GO term definitions)

Chain A,B (THBG_HUMAN | P05543)

molecular function
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0070327	thyroid hormone transport	The directed movement of thyroid hormone into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2riv)

Biological Units
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	2riv
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	THBG_HUMAN \| P05543
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	THBG_HUMAN \| P05543
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UniProtKB/Swiss-Prot
	THBG_HUMAN \| P05543	:	2ceo 2riw 2xn3 2xn5 2xn6 2xn7 4x30 4yia

2riw	THE SAME PROTEIN COMPLEXED WITH THYROXINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (9, 10)

PROSITE Motifs (1, 1)

Exons (4, 5)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File