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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF HUMAN CHORIONIC GONADOTROPIN AT 2.6 ANGSTROMS RESOLUTION FROM MAD ANALYSIS OF THE SELENOMETHIONYL PROTEIN

Authors :   H. Wu, J. W. Lustbader, Y. Liu, R. E. Canfield, W. A. Hendrickson

Date :   01 Jul 94 (Deposition) - 30 Sep 94 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Hormone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Wu, J. W. Lustbader, Y. Liu, R. E. Canfield, W. A. Hendrickson
Structure Of Human Chorionic Gonadotropin At 2. 6 A Resolution From Mad Analysis Of The Selenomethionyl Protein
Structure V. 2 545 1994
PubMed-ID: 7922031 | Reference-DOI: 10.1016/S0969-2126(00)00054-X
(for further references see the PDB file header)

Molecule 1 - HUMAN CHORIONIC GONADOTROPIN
	Chains	:	A
	Engineered	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - HUMAN CHORIONIC GONADOTROPIN
	Chains	:	B
	Engineered	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:52 , VAL A:53 , TYR B:59 , VAL B:62 , PHE B:64 , ALA B:83	BINDING SITE FOR RESIDUE NAG A 93
2	AC2	SOFTWARE	ALA A:23 , PRO A:24 , ILE A:25 , ASN A:78	BINDING SITE FOR RESIDUE NAG A 94

Asymmetric Unit

No.	Residues
1	A:7	-	A:31
2	A:10	-	A:60
3	A:28	-	A:82
4	A:32	-	A:84
5	A:59	-	A:87
6	B:9	-	B:57
7	B:23	-	B:72
8	B:26	-	B:110
9	B:34	-	B:88
10	B:38	-	B:90
11	B:93	-	B:100

Asymmetric Unit

No.	Residues
1	Leu B:49	-	Pro B:50

Asymmetric Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_014586	K	22	R	CGB3_HUMAN	Polymorphism	6518	B	K	2	R
2	UniProt	VAR_015232	P	24	M	CGB3_HUMAN	Unclassified	---	B	P	4	M
3	UniProt	VAR_015233	R	28	W	CGB3_HUMAN	Polymorphism	---	B	R	8	W
4	UniProt	VAR_015234	R	30	H	CGB3_HUMAN	Polymorphism	201373221	B	R	10	H
5	UniProt	VAR_014587	T	35	I	CGB3_HUMAN	Polymorphism	6515	B	T	15	I
6	UniProt	VAR_014588	N	97	D	CGB3_HUMAN	Polymorphism	6519	B	N	77	D

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

Biological Unit 1 (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_014586	K	22	R	CGB3_HUMAN	Polymorphism	6518	B	K	2	R
2	UniProt	VAR_015232	P	24	M	CGB3_HUMAN	Unclassified	---	B	P	4	M
3	UniProt	VAR_015233	R	28	W	CGB3_HUMAN	Polymorphism	---	B	R	8	W
4	UniProt	VAR_015234	R	30	H	CGB3_HUMAN	Polymorphism	201373221	B	R	10	H
5	UniProt	VAR_014587	T	35	I	CGB3_HUMAN	Polymorphism	6515	B	T	15	I
6	UniProt	VAR_014588	N	97	D	CGB3_HUMAN	Polymorphism	6519	B	N	77	D

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

Biological Unit 2 (6, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_014586	K	22	R	CGB3_HUMAN	Polymorphism	6518	B	K	2	R
2	UniProt	VAR_015232	P	24	M	CGB3_HUMAN	Unclassified	---	B	P	4	M
3	UniProt	VAR_015233	R	28	W	CGB3_HUMAN	Polymorphism	---	B	R	8	W
4	UniProt	VAR_015234	R	30	H	CGB3_HUMAN	Polymorphism	201373221	B	R	10	H
5	UniProt	VAR_014587	T	35	I	CGB3_HUMAN	Polymorphism	6515	B	T	15	I
6	UniProt	VAR_014588	N	97	D	CGB3_HUMAN	Polymorphism	6519	B	N	77	D

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

Asymmetric Unit (5, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCO_HORMONE_ALPHA_3	PS50277	Glycoprotein hormones alpha chain family profile.	GLHA_HUMAN	31-116	1	A:7-89
2	GLYCO_HORMONE_ALPHA_1	PS00779	Glycoprotein hormones alpha chain signature 1.	GLHA_HUMAN	52-64	1	A:28-40
3	GLYCO_HORMONE_BETA_1	PS00261	Glycoprotein hormones beta chain signature 1.	CGB3_HUMAN	54-60	1	B:34-40
3	GLYCO_HORMONE_BETA_1	PS00261	Glycoprotein hormones beta chain signature 1.	CGB7_HUMAN	54-60	1	B:34-40
4	GLYCO_HORMONE_ALPHA_2	PS00780	Glycoprotein hormones alpha chain signature 2.	GLHA_HUMAN	102-115	1	A:78-89
5	GLYCO_HORMONE_BETA_2	PS00689	Glycoprotein hormones beta chain signature 2.	CGB3_HUMAN	103-130	1	B:83-110
5	GLYCO_HORMONE_BETA_2	PS00689	Glycoprotein hormones beta chain signature 2.	CGB7_HUMAN	103-130	1	B:83-110

Biological Unit 1 (5, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCO_HORMONE_ALPHA_3	PS50277	Glycoprotein hormones alpha chain family profile.	GLHA_HUMAN	31-116	1	A:7-89
2	GLYCO_HORMONE_ALPHA_1	PS00779	Glycoprotein hormones alpha chain signature 1.	GLHA_HUMAN	52-64	1	A:28-40
3	GLYCO_HORMONE_BETA_1	PS00261	Glycoprotein hormones beta chain signature 1.	CGB3_HUMAN	54-60	1	B:34-40
3	GLYCO_HORMONE_BETA_1	PS00261	Glycoprotein hormones beta chain signature 1.	CGB7_HUMAN	54-60	1	B:34-40
4	GLYCO_HORMONE_ALPHA_2	PS00780	Glycoprotein hormones alpha chain signature 2.	GLHA_HUMAN	102-115	1	A:78-89
5	GLYCO_HORMONE_BETA_2	PS00689	Glycoprotein hormones beta chain signature 2.	CGB3_HUMAN	103-130	1	B:83-110
5	GLYCO_HORMONE_BETA_2	PS00689	Glycoprotein hormones beta chain signature 2.	CGB7_HUMAN	103-130	1	B:83-110

Biological Unit 2 (5, 14)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCO_HORMONE_ALPHA_3	PS50277	Glycoprotein hormones alpha chain family profile.	GLHA_HUMAN	31-116	2	A:7-89
2	GLYCO_HORMONE_ALPHA_1	PS00779	Glycoprotein hormones alpha chain signature 1.	GLHA_HUMAN	52-64	2	A:28-40
3	GLYCO_HORMONE_BETA_1	PS00261	Glycoprotein hormones beta chain signature 1.	CGB3_HUMAN	54-60	2	B:34-40
3	GLYCO_HORMONE_BETA_1	PS00261	Glycoprotein hormones beta chain signature 1.	CGB7_HUMAN	54-60	2	B:34-40
4	GLYCO_HORMONE_ALPHA_2	PS00780	Glycoprotein hormones alpha chain signature 2.	GLHA_HUMAN	102-115	2	A:78-89
5	GLYCO_HORMONE_BETA_2	PS00689	Glycoprotein hormones beta chain signature 2.	CGB3_HUMAN	103-130	2	B:83-110
5	GLYCO_HORMONE_BETA_2	PS00689	Glycoprotein hormones beta chain signature 2.	CGB7_HUMAN	103-130	2	B:83-110

Asymmetric Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000369582	1	ENSE00001450387	chr6:87804824-87804731	94	GLHA_HUMAN	-	0	0	-	-
1.2	ENST00000369582	2	ENSE00000798150	chr6:87797925-87797831	95	GLHA_HUMAN	1-30	30	1	A:5-6	2
1.3	ENST00000369582	3	ENSE00000798149	chr6:87796152-87795968	185	GLHA_HUMAN	30-91	62	1	A:6-67	62
1.4	ENST00000369582	4	ENSE00000798148	chr6:87795551-87795216	336	GLHA_HUMAN	92-116	25	1	A:68-89	22

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:85
 aligned with GLHA_HUMAN | P01215 from UniProtKB/Swiss-Prot  Length:116

    Alignment length:85
                                    38        48        58        68        78        88        98       108     
           GLHA_HUMAN    29 QDCPECTLQENPFFSQPGAPILQCMGCCFSRAYPTPLRSKKTMLVQKNVTSESTCCVAKSYNRVTVMGGFKVENHTACHCSTCYY 113
               SCOP domains d1hcna_ A: Glycoprotein hormones alpha chain (Gonadotropin A, Follitropin alpha)      SCOP domains
               CATH domains 1hcnA00 A:5-89 Cystine-knot cytokines                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.........eeeeeeeeeeeeeeehhhhhhhh....eeeeeee............................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --GLYCO_HORMONE_ALPHA_3  PDB: A:7-89 UniProt: 31-116                                  PROSITE (1)
                PROSITE (2) -----------------------GLYCO_HORMONE-------------------------------------GLYCO_HORMON PROSITE (2)
           Transcript 1 (1) 1.-------------------------------------------------------------Exon 1.4  PDB: A:68-89 Transcript 1 (1)
           Transcript 1 (2) -Exon 1.3  PDB: A:6-67 UniProt: 30-91                          ---------------------- Transcript 1 (2)
                 1hcn A   5 QDCPECTLQENPFFSQPGAPILQCMGCCFSRAYPTPLRSKKTMLVQKNVTSESTCCVAKSYNRVTVMGGFKVENHTACHCSTCYY  89
                                    14        24        34        44        54        64        74        84

Chain B from PDB  Type:PROTEIN  Length:110
 aligned with CGB3_HUMAN | P0DN86 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:110
                                    31        41        51        61        71        81        91       101       111       121       131
           CGB3_HUMAN    22 KEPLRPRCRPINATLAVEKEGCPVCITVNTTICAGYCPTMTRVLQGVLPALPQVVCNYRDVRFESIRLPGCPRGVNPVVSYAVALSCQCALCRRSTTDCGGPKDHPLTCD 131
               SCOP domains d1hcnb_ B: Gonadotropin B chain                                                                                SCOP domains
               CATH domains 1hcnB00 B:2-111 Cystine-knot cytokines                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeee........eeeeeeeeeeeeee..........................................................eee.......... Sec.struct. author
                 SAPs(SNPs) R-M---W-H----I-------------------------------------------------------------D---------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------GLYCO_H------------------------------------------GLYCO_HORMONE_BETA_2        - PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1hcn B   2 KEPLRPRCRPINATLAVEKEGCPVCITVNTTICAGYCPTMTRVLQGVLPALPQVVCNYRDVRFESIRLPGCPRGVNPVVSYAVALSCQCALCRRSTTDCGGPKDHPLTCD 111
                                    11        21        31        41        51        61        71        81        91       101       111

Chain B from PDB  Type:PROTEIN  Length:110
 aligned with CGB7_HUMAN | P0DN87 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:110
                                    31        41        51        61        71        81        91       101       111       121       131
           CGB7_HUMAN    22 REMLRPRCRPINATLAVEKEGCPVCITVNTTICAGYCPTMTRVLQGVLPALPQVVCNYRDVRFESIRLPGCPRGVNPVVSYAVALSCQCALCRRSTTDCGGPKDHPLTCD 131
               SCOP domains d1hcnb_ B: Gonadotropin B chain                                                                                SCOP domains
               CATH domains 1hcnB00 B:2-111 Cystine-knot cytokines                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeee........eeeeeeeeeeeeee..........................................................eee.......... Sec.struct. author
                 SAPs(SNPs) R-M---W-H----I-------------------------------------------------------------D---------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------GLYCO_H------------------------------------------GLYCO_HORMONE_BETA_2        - PROSITE (4)
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1hcn B   2 KEPLRPRCRPINATLAVEKEGCPVCITVNTTICAGYCPTMTRVLQGVLPALPQVVCNYRDVRFESIRLPGCPRGVNPVVSYAVALSCQCALCRRSTTDCGGPKDHPLTCD 111
                                    11        21        31        41        51        61        71        81        91       101       111

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Cystine Knot Cytokines, subunit B (102)

Homologous Superfamily: Cystine-knot cytokines (102)

Human (Homo sapiens) (84)

1a	1hcnB00	B:2-111
1b	1hcnA00	A:5-89

(no "Pfam Domain" information available for 1HCN)

Asymmetric Unit(hide GO term definitions)

Chain A (GLHA_HUMAN | P01215)

molecular function
	GO:0005179	hormone activity	The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	GO:0016486	peptide hormone processing	The generation of a mature peptide hormone by posttranslational processing of a prohormone.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0005796	Golgi lumen	The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
	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.

Chain B (CGB7_HUMAN | P0DN87)

molecular function
	GO:0005179	hormone activity	The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
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.

Chain B (CGB3_HUMAN | P0DN86)

molecular function
	GO:0005179	hormone activity	The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
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.

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(no "Related Entries Specified in the PDB File" available for 1HCN)

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SS Bonds (11, 11)

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