PDB-4e4d: Crystal structure of mouse RANKL-OPG complex

Basic information

• Entry: Database: PDB / ID: 4e4d
• Title: Crystal structure of mouse RANKL-OPG complex

Components

• Tumor necrosis factor ligand superfamily member 11, soluble form
• Tumor necrosis factor receptor superfamily member 11B

• Keywords: Cytokine/Signaling Protein / TNF-Related Activation-Induced Cytokine-Receptor / Cysteine-Rich Domain / Jelly-Roll Fold / Cytokine-Signaling Protein complex

Function / homology

Function:

positive regulation of corticotropin-releasing hormone secretion / positive regulation of fever generation by positive regulation of prostaglandin secretion / negative regulation of odontogenesis of dentin-containing tooth / tooth eruption / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / osteoclast proliferation / TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / positive regulation of osteoclast development / TNFR2 non-canonical NF-kB pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / regulation of osteoclast differentiation / positive regulation of homotypic cell-cell adhesion / osteoclast development / paracrine signaling / response to arsenic-containing substance / heparan sulfate binding / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / negative regulation of bone resorption / mammary gland epithelial cell proliferation / negative regulation of osteoclast differentiation / monocyte chemotaxis / response to magnesium ion / mammary gland alveolus development / negative regulation of tumor necrosis factor-mediated signaling pathway / lymph node development / positive regulation of bone resorption / bone resorption / positive regulation of phosphorylation / calcium ion homeostasis / tumor necrosis factor-mediated signaling pathway / JNK cascade / extracellular matrix organization / response to nutrient / ERK1 and ERK2 cascade / extracellular matrix / osteoclast differentiation / ossification / cellular response to leukemia inhibitory factor / positive regulation of DNA-binding transcription factor activity / animal organ morphogenesis / cytokine activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of JNK cascade / calcium-mediated signaling / bone development / positive regulation of T cell activation / response to estrogen / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of ERK1 and ERK2 cascade / immune response / receptor ligand activity / response to xenobiotic stimulus / apoptotic process / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / plasma membrane / cytoplasm

Domain/homology:

Tumour necrosis factor receptor 11B / Tumor Necrosis Factor Receptor Superfamily Member 11B death domain / Tumour necrosis factor receptor 11 / : / Tumour necrosis factor ligand 10/11 / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region domain profile. / Tumour necrosis factor domain / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Putative ephrin-receptor like / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death-like domain superfamily / Ribbon / Jelly Rolls / Sandwich / Mainly Beta

Component:

Tumor necrosis factor receptor superfamily member 11B / Tumor necrosis factor ligand superfamily member 11

• Biological species: Mus musculus (house mouse)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
• Authors: Nelson, C.A. / Fremont, D.H.
• Citation: Journal: Structure / Year: 2012; Title: RANKL Employs Distinct Binding Modes to Engage RANK and the Osteoprotegerin Decoy Receptor.; Authors: Nelson, C.A. / Warren, J.T. / Wang, M.W. / Teitelbaum, S.L. / Fremont, D.H.

History

Deposition	Mar 12, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 24, 2012	Provider: repository / Type: Initial release
Revision 1.1	Dec 12, 2012	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Sep 13, 2023	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Assembly

Deposited unit

X: Tumor necrosis factor ligand superfamily member 11, soluble form

R: Tumor necrosis factor receptor superfamily member 11B

hetero molecules

Summary:

• 37.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	37,820	4
Polymers	37,749	2
Non-polymers	71	2
Water	1,675	93

1

X: Tumor necrosis factor ligand superfamily member 11, soluble form

hetero molecules

X: Tumor necrosis factor ligand superfamily member 11, soluble form

R: Tumor necrosis factor receptor superfamily member 11B

hetero molecules

X: Tumor necrosis factor ligand superfamily member 11, soluble form

R: Tumor necrosis factor receptor superfamily member 11B

hetero molecules

Summary:

• defined by author
• 93.1 kDa, 5 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	93,086	11
Polymers	92,874	5
Non-polymers	213	6
Water	90	5

Symmetry operations:

Type	Name	Symmetry operation	Number
crystal symmetry operation	3_665	-x+y+1,-x+1,z	1
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_655	-y+1,x-y,z	1

2

X: Tumor necrosis factor ligand superfamily member 11, soluble form

R: Tumor necrosis factor receptor superfamily member 11B

hetero molecules

X: Tumor necrosis factor ligand superfamily member 11, soluble form

R: Tumor necrosis factor receptor superfamily member 11B

hetero molecules

X: Tumor necrosis factor ligand superfamily member 11, soluble form

R: Tumor necrosis factor receptor superfamily member 11B

hetero molecules

Summary:

• defined by software
• 113 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	113,459	12
Polymers	113,246	6
Non-polymers	213	6
Water	108	6

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_655	-y+1,x-y,z	1
crystal symmetry operation	3_665	-x+y+1,-x+1,z	1

Calculated values:

Buried area	13600 Å2
ΔGint	-111 kcal/mol
Surface area	40040 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	109.763, 109.763, 78.800
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P63

Components

#1: Protein

X Tumor necrosis factor ligand superfamily member 11, soluble form / Osteoclast differentiation factor / ODF / Osteoprotegerin ligand / OPGL / Receptor activator of nuclear factor kappa-B ligand / RANKL / TNF-related activation-induced cytokine / TRANCE /

Details:

Mass: 17376.463 Da / Num. of mol.: 1 / Fragment: UNP residues 162-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CD254, ODF, Opgl, Rankl, Tnfsf11, Trance / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21CodonPlus(DE3)-RIL / References: UniProt: O35235

#2: Protein

R Tumor necrosis factor receptor superfamily member 11B / Osteoclastogenesis inhibitory factor / Osteoprotegerin

Details:

Mass: 20372.166 Da / Num. of mol.: 1 / Fragment: UNP residues 22-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 B / Gene: Ocif, Opg, Osteoprotegerin, Tnfrsf11b / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HIGH FIVE / References: UniProt: O08712

#3: Chemical

X-401 X-402 ChemComp-CL / CHLORIDE ION

Details:

Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

#4: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H₂O

• Has protein modification: Y

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 3.71 ų/Da / Density % sol: 66.83 %
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.1 ; Details: 100 mM sodium phosphate/citrate buffer, 14% polyethylene glycol 8000 and 250 mM sodium chloride, pH 4.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9951 Å
• Detector: Type: NOIR-1 / Detector: CCD / Date: Jan 1, 2007
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9951 Å / Relative weight: 1
• Reflection: Resolution: 2.7→50 Å / Num. obs: 14915 / % possible obs: 99.3 % / Redundancy: 2.9 % / B_iso Wilson estimate: 48.42 Ų / R_merge(I) obs: 0.084 / Net I/σ(I): 12.8

Reflection shell

Resolution (Å)	Redundancy (%)	Rmerge(I) obs	Diffraction-ID	% possible all
2.7-2.8	2.8	0.563	1	100
2.8-2.91	2.8	0.385	1	100
2.91-3.04	2.9	0.281	1	100
3.04-3.2	2.9	0.19	1	100
3.2-3.4	2.8	0.141	1	100
3.4-3.66	2.9	0.117	1	99.8
3.66-4.03	2.9	0.089	1	99.4
4.03-4.62	2.8	0.062	1	99.7
4.62-5.81	2.9	0.048	1	98.9
5.81-50	2.9	0.029	1	95.6

Processing

Software

Name	Version	Classification	NB
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.1	data extraction
Blu-Ice		data collection
SHARP		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JTZ

1jtz

Resolution: 2.7→40.7 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / Phase error: 23.59 / Stereochemistry target values: ML

	Rfactor	Num. reflection	% reflection
Rfree	0.23	1476	10.15 %
Rwork	0.194	-	-
obs	0.202	14542	97.1 %
all	-	42626	-

• Solvent computation: Solvent model: FLAT BULK SOLVENT MODEL
• Displacement parameters: B_iso mean: 71.12 Ų

Refinement step

Cycle: LAST / Resolution: 2.7→40.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2277	0	2	93	2372

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	2348
X-RAY DIFFRACTION	f_angle_d	0.593	3171
X-RAY DIFFRACTION	f_dihedral_angle_d	9.943	852
X-RAY DIFFRACTION	f_chiral_restr	0.04	336
X-RAY DIFFRACTION	f_plane_restr	0.003	411

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
2.7-2.7871	0.2833	127	0.2377	1111	X-RAY DIFFRACTION	92
2.7871-2.8867	0.284	114	0.2338	1164	X-RAY DIFFRACTION	95
2.8867-3.0023	0.2817	135	0.2209	1172	X-RAY DIFFRACTION	96
3.0023-3.1389	0.2501	133	0.2078	1178	X-RAY DIFFRACTION	97
3.1389-3.3043	0.2623	130	0.2075	1209	X-RAY DIFFRACTION	99
3.3043-3.5112	0.2193	117	0.2008	1212	X-RAY DIFFRACTION	99
3.5112-3.7821	0.231	148	0.184	1202	X-RAY DIFFRACTION	100
3.7821-4.1624	0.2332	130	0.1704	1203	X-RAY DIFFRACTION	98
4.1624-4.7639	0.183	157	0.1611	1209	X-RAY DIFFRACTION	99
4.7639-5.9989	0.221	123	0.1925	1228	X-RAY DIFFRACTION	99
5.9989-40.7034	0.266	162	0.2367	1178	X-RAY DIFFRACTION	95

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°2)	L12 (°2)	L13 (°2)	L22 (°2)	L23 (°2)	L33 (°2)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å2)	T12 (Å2)	T13 (Å2)	T22 (Å2)	T23 (Å2)	T33 (Å2)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	8.5775	1.5397	-2.2381	2.8355	0.7563	2.615	0.6831	-1.3538	-0.4485	0.2598	-0.4248	-0.2471	1.1337	1.2059	-0.3246	1.1839	0.0909	-0.1425	0.8077	0.1274	0.6357	66.6807	-1.0808	27.5509
2	0.5559	0.093	1.3943	2.2446	-0.3416	3.647	0.0777	0.1495	-0.2255	0.0877	-0.2212	0.0757	1.4948	0.5157	0.1358	1.2571	0.0809	0.0459	0.5755	-0.034	0.7069	58.6539	2.4119	4.5034
3	4.5249	-0.1382	-4.0095	2.9653	0.0742	6.6838	-0.0658	0.5958	0.2261	-0.9342	0.5103	-1.4353	0.9482	1.9733	-0.3192	1.0908	0.1073	0.2499	1.1385	-0.2232	0.8206	68.7473	10.847	-18.4317
4	0.2621	-1.4365	0.6996	8.1575	-2.7393	6.0877	0.549	0.5597	0.0664	-1.4366	-1.0267	-0.4104	0.998	0.5623	0.0501	1.7367	-0.5512	0.5491	2.557	-0.5889	1.1461	82.8869	11.2919	-29.3658
5	6.4417	-5.5088	-4.351	4.8215	4.1762	4.8081	-0.0515	-0.0599	0.279	0.3516	0.4126	-0.3805	-0.5967	0.1375	-0.5055	1.3552	-0.1326	0.3453	1.4101	-0.0366	1.3504	76.5962	7.6354	-33.8245
6	4.0371	0.807	5.3166	9.1108	1.4757	8.6848	0.1231	0.7271	-0.5028	-0.6051	0.1119	-1.1943	0.5268	1.6495	-0.2257	0.358	0.0008	-0.04	0.5204	0.0613	0.6134	72.151	29.2634	4.8917
7	2.8013	0.2372	-0.6458	3.778	-0.0455	3.338	0.0219	-0.171	-0.319	0.2644	-0.1318	-0.5742	0.2375	1.2025	0.1355	0.3024	0.0097	0.0102	0.5735	0.051	0.3619	69.5004	28.7157	7.936
8	2	7.6293	-5.7892	6.061	-5.5645	6.3118	0.909	-0.8568	1.0134	1.3388	0.3576	0.2483	-1.093	-0.2267	-1.1278	1.6324	-0.4565	0.291	2.1203	0.075	0.9474	68.2566	31.4592	-25.0154
9	5.6644	0.8088	-0.2015	4.7526	0.6604	3.5115	0.0375	0.4758	-0.5162	-0.5537	-0.1493	-0.2563	0.7509	0.7274	0.2082	0.4292	0.0097	0.0655	0.2559	-0.0831	0.3406	63.0837	20.9015	-2.4835
10	2.5824	0.0776	-0.0368	4.4716	0.642	4.9911	-0.0348	-0.0523	0.0026	0.0052	-0.0134	-0.0507	0.205	0.6225	0.063	0.1489	0.006	-0.028	0.3046	0.013	0.3058	64.2693	28.0275	4.7835

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain R and resid 7:39)	R	7 - 39
2	X-RAY DIFFRACTION	2	(chain R and resid 40:88)	R	40 - 88
3	X-RAY DIFFRACTION	3	(chain R and resid 89:121)	R	89 - 121
4	X-RAY DIFFRACTION	4	(chain R and resid 122:125)	R	122 - 125
5	X-RAY DIFFRACTION	5	(chain R and resid 126:141)	R	126 - 141
6	X-RAY DIFFRACTION	6	(chain X and resid 162:179)	X	162 - 179
7	X-RAY DIFFRACTION	7	(chain X and resid 180:226)	X	180 - 226
8	X-RAY DIFFRACTION	8	(chain X and resid 227:232)	X	227 - 232
9	X-RAY DIFFRACTION	9	(chain X and resid 233:266)	X	233 - 266
10	X-RAY DIFFRACTION	10	(chain X and resid 267:315)	X	267 - 315