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- PDB-6mi2: Structure of the human 4-1BB / Utomilumab Fab complex -

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Basic information

Entry
Database: PDB / ID: 6mi2
TitleStructure of the human 4-1BB / Utomilumab Fab complex
Components
  • (Utomilumab Fab ...) x 2
  • Tumor necrosis factor receptor superfamily member 9
KeywordsIMMUNE SYSTEM / Signaling / TNFRSF / 4-1BB / CD137 / therapeutic antibody / complex
Function / homology
Function and homology information


TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / signaling receptor activity / regulation of cell population proliferation / negative regulation of cell population proliferation / external side of plasma membrane / apoptotic process / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 9 / Tumour necrosis factor receptor 9, N-terminal / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Growth factor receptor cysteine-rich domain superfamily ...Tumour necrosis factor receptor 9 / Tumour necrosis factor receptor 9, N-terminal / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Growth factor receptor cysteine-rich domain superfamily / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 Å
AuthorsKimberlin, C.R. / Chin, S.M. / Roe-Zurz, Z. / Xu, A. / Yang, Y.
CitationJournal: Nat Commun / Year: 2018
Title: Structure of the 4-1BB/4-1BBL complex and distinct binding and functional properties of utomilumab and urelumab.
Authors: Chin, S.M. / Kimberlin, C.R. / Roe-Zurz, Z. / Zhang, P. / Xu, A. / Liao-Chan, S. / Sen, D. / Nager, A.R. / Oakdale, N.S. / Brown, C. / Wang, F. / Yang, Y. / Lindquist, K. / Yeung, Y.A. / ...Authors: Chin, S.M. / Kimberlin, C.R. / Roe-Zurz, Z. / Zhang, P. / Xu, A. / Liao-Chan, S. / Sen, D. / Nager, A.R. / Oakdale, N.S. / Brown, C. / Wang, F. / Yang, Y. / Lindquist, K. / Yeung, Y.A. / Salek-Ardakani, S. / Chaparro-Riggers, J.
History
DepositionSep 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Utomilumab Fab heavy chain
B: Utomilumab Fab lambda chain
D: Utomilumab Fab heavy chain
E: Utomilumab Fab lambda chain
F: Tumor necrosis factor receptor superfamily member 9
C: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,70337
Polymers126,3656
Non-polymers3,33931
Water82946
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A: Utomilumab Fab heavy chain
B: Utomilumab Fab lambda chain
C: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,39325
Polymers63,1823
Non-polymers2,21122
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Utomilumab Fab heavy chain
E: Utomilumab Fab lambda chain
F: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,31012
Polymers63,1823
Non-polymers1,1289
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.903, 73.338, 175.121
Angle α, β, γ (deg.)90.000, 98.990, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 2 molecules FC

#3: Protein Tumor necrosis factor receptor superfamily member 9 / 4-1BB ligand receptor / CDw137 / T-cell antigen 4-1BB homolog / T-cell antigen ILA


Mass: 15727.700 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF9, CD137, ILA / Plasmid: pFastBac / Cell line (production host): HighFive / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q07011

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Antibody , 2 types, 4 molecules ADBE

#1: Antibody Utomilumab Fab heavy chain


Mass: 24755.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Utomilumab Fab lambda chain


Mass: 22698.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 75 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.5M lithium sulfate, 0.1M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.72→49.303 Å / Num. obs: 46410 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.985 / Rmerge(I) obs: 0.35 / Rpim(I) all: 0.143 / Rrim(I) all: 0.379 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.72-2.8274.50944970.2351.8244.869100
10.53-49.36.30.0378460.9990.0160.04198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→49.303 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.97
RfactorNum. reflection% reflection
Rfree0.2778 1979 4.29 %
Rwork0.2383 --
obs0.24 46170 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 194.05 Å2 / Biso mean: 86.6898 Å2 / Biso min: 15.94 Å2
Refinement stepCycle: final / Resolution: 2.72→49.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7881 0 192 46 8119
Biso mean--113.65 51.22 -
Num. residues----1115
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.72-2.7880.42361240.38442982310694
2.788-2.86340.39321400.38483103324399
2.8634-2.94770.43341430.369131673310100
2.9477-3.04280.41271400.352931273267100
3.0428-3.15150.35941400.31731103250100
3.1515-3.27770.35361430.292731743317100
3.2777-3.42680.28631410.266231513292100
3.4268-3.60740.30151430.232931753318100
3.6074-3.83340.27391430.228331553298100
3.8334-4.12920.24491430.198631803323100
4.1292-4.54450.1961440.167531923336100
4.5445-5.20150.2391440.180431833327100
5.2015-6.55090.26581440.220632083352100
6.5509-49.3110.22931470.221632843431100
Refinement TLS params.

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

IDL11 (°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)
13.117-0.36311.15111.1516-0.25263.89070.15280.42880.2132-0.2877-0.0772-0.56690.13330.2705-0.04140.39830.02110.19310.26820.03610.6087-10.6253-15.5439-56.2829
22.91361.41350.14672.77391.90513.5372-0.12311.32190.4110.02910.32630.02480.6947-0.3083-0.19270.6385-0.0640.18061.11580.16960.6703-31.761-8.9395-82.0743
30.36740.3791.01743.7996-0.82784.2590.12790.09080.2805-0.2292-0.2716-0.26860.13280.4184-0.10730.3048-0.06740.18130.111-0.01571.379-33.3057-8.9886-45.7323
45.874-1.54981.5742.3026-1.17193.8625-0.0019-0.32730.7833-0.18630.04290.26640.1255-0.0207-0.22040.2143-0.0034-0.04290.1679-0.00620.3245-24.0927-8.7108-42.7783
53.0042-3.15040.48474.1819-2.78246.0933-0.1721-0.0041.53420.62040.2064-0.0793-0.80640.231-0.08360.35660.0427-0.10940.2653-0.06591.0073-21.85460.8273-37.2474
62.6482-0.4062-0.31791.6592-0.06841.2258-0.07750.07560.4710.13630.04420.3639-0.1052-0.02090.03790.2112-0.0647-0.01260.28220.02670.8657-28.9635-7.1701-45.3946
75.3032-3.4761-3.38034.23424.8295.6542-0.37520.39830.37670.614-0.5895-0.04360.59680.1160.73841.0588-0.2032-0.01030.8180.17670.9407-38.9344-20.3501-81.1818
84.0402-0.9292-0.76261.60550.3183.3656-0.44410.6883-0.10370.65360.55770.62971.1391-1.0735-0.23040.7827-0.23990.09290.61020.13380.8303-38.9733-14.6392-67.0093
96.4588-0.16671.23064.31880.89823.95580.03730.98310.263-0.6767-0.29-0.34120.7620.46430.12730.9301-0.0940.12420.6536-0.0180.4416-35.1018-14.5608-67.898
104.1243-2.1277-2.9662.3033.78056.7231-0.02710.1636-1.2357-0.72790.2439-0.05391.491-0.1833-0.17571.5381-0.1825-0.19220.443-0.06780.7746-41.5926-26.1059-72.021
113.85681.0888-0.04762.68140.14074.5951-0.41990.6942-0.221-0.46570.0127-0.01680.2454-0.4837-0.62331.0014-0.3006-0.30970.94120.09020.3348-46.3866-18.2849-65.9652
123.8021-0.8122-1.28652.5209-0.9334.06190.22250.46660.1828-0.4725-0.1547-0.2797-0.07520.1413-0.11370.40270.0513-0.01230.3971-0.06270.809226.047622.4343-59.9142
133.19061.20841.0912.8912-2.48013.7943-0.16410.7623-0.21340.0810.10390.0892-0.5071-0.0551-0.06620.64650.02620.17431.1457-0.35890.784355.878415.3086-79.2456
142.73470.56171.98112.3092-0.79863.8793-0.1458-0.09670.68750.01150.6392-0.44330.20810.2658-0.68190.34650.0058-0.06020.62480.13161.229345.083314.1728-42.5977
153.2007-0.58210.43963.00690.1423.44660.09320.0759-0.88280.22320.2286-0.39060.17550.4665-0.25010.33410.0530.06170.4791-0.01131.023634.906610.4149-41.6537
162.83250.10731.71452.1617-0.32512.627-0.29470.0794-1.14950.0014-0.0139-0.03890.04170.24250.26240.32480.0224-0.00960.4382-0.05291.1441.767412.2085-47.805
173.055-0.1776-0.39822.6135-2.96385.24190.23420.63310.05070.6702-0.1498-0.9209-1.57770.3765-0.11581.0793-0.22320.02060.8042-0.32780.929662.008922.2463-66.8229
182.0176-0.71391.39470.2916-0.54171.0106-0.28970.32260.0110.2524-0.1316-0.1190.12840.02260.40991.0256-0.3409-0.06160.8468-0.28841.112669.460320.0002-61.508
197.0874-4.6843-6.14944.08014.765.89230.01910.2189-0.3029-1.2559-1.37680.65640.8953-0.40931.03091.27910.0223-0.33110.9479-0.05161.118131.4885-23.5287-61.8721
208.9713-6.90530.03669.47265.19986.5465-0.58461.1-0.8316-0.1361-0.20672.0303-0.0332-0.36440.81330.5982-0.2660.02250.63290.00771.09932.5117-26.3356-53.3239
218.6448-6.5944-3.60686.47172.00743.7519-0.24650.820.1235-1.22551.38030.1629-1.19460.148-0.82850.8482-0.30480.01050.8564-0.06941.09231.398-17.4815-55.6757
224.8857-6.6032-1.37128.96862.04461.6462-0.6652-0.28260.66930.63231.12391.4075-0.11930.2193-0.18450.75510.1905-0.12280.7876-0.02861.482621.3722-7.204-43.6856
231.54652.2313-0.42094.4696-0.89515.8607-0.54040.3779-0.37140.08790.00840.70.2239-0.31290.12581.2565-0.1291-0.06390.6088-0.24482.230221.6202-14.0468-50.946
244.6765-3.0043-2.78182.60313.53056.3839-0.40010.4444-0.62541.18960.15450.39571.3363-0.23670.03830.61610.02460.1650.4880.05331.592116.91825.3204-42.5683
250.6180.639-0.63151.0407-0.12381.48070.22940.17760.18860.0503-0.21190.01030.16670.5622-0.13220.04340.37270.42460.4147-0.05661.775712.126322.077-40.1673
262.8493.64830.73847.5761.660.4017-0.41810.20331.3221-0.2334-0.2649-0.41180.180.27130.95460.5836-0.09910.17550.59090.18841.22110.650335.6056-48.7473
270.7922-0.63760.31573.903-2.97534.9575-0.33880.6906-0.2953-0.150.20970.42670.1159-0.99650.04150.224-0.0221-0.1020.62220.05051.50691.742827.7344-45.4087
284.255-1.1059-1.92963.9598-1.99614.73430.0480.6122-0.511-0.14560.0031-0.22930.163-0.1669-0.050.4144-0.00570.0190.3833-0.07051.2129-12.706827.6108-49.7234
290.6092-1.11160.52386.7802-5.39075.94650.3911-0.0712-0.00621.0659-0.08850.2644-0.15460.3158-0.44810.47090.01710.07440.4401-0.1461.3025-9.619413.3229-35.9157
301.08971.78810.54974.8561-1.74495.38210.15030.1443-0.26450.4095-0.0369-0.78590.34890.5333-0.43910.2640.0613-0.07270.2624-0.07850.3188-7.9093-2.2172-32.1864
315.4166-5.6538-0.44127.50821.35221.6432-0.5746-0.3263-1.57420.5520.42240.68280.52320.06580.07970.37780.1226-0.0850.35180.00940.6749-5.5136-19.8496-30.6469
320.293-0.4503-0.01360.99680.12670.3216-0.2219-0.0723-0.283-0.2799-0.19850.4044-0.079-0.17540.03090.70610.22520.17130.446-0.03281.69378.0282-33.8129-34.843
334.5723-4.0305-1.22743.68640.72451.3144-0.3857-0.2157-1.01820.24210.0644-0.04170.44910.3210.07230.46230.1391-0.09470.6416-0.05711.554511.6027-32.9182-36.6752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 140 )A1 - 140
2X-RAY DIFFRACTION2chain 'A' and (resid 141 through 217 )A141 - 217
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 17 )B1 - 17
4X-RAY DIFFRACTION4chain 'B' and (resid 18 through 47 )B18 - 47
5X-RAY DIFFRACTION5chain 'B' and (resid 48 through 60 )B48 - 60
6X-RAY DIFFRACTION6chain 'B' and (resid 61 through 115 )B61 - 115
7X-RAY DIFFRACTION7chain 'B' and (resid 116 through 131 )B116 - 131
8X-RAY DIFFRACTION8chain 'B' and (resid 132 through 152 )B132 - 152
9X-RAY DIFFRACTION9chain 'B' and (resid 153 through 182 )B153 - 182
10X-RAY DIFFRACTION10chain 'B' and (resid 183 through 199 )B183 - 199
11X-RAY DIFFRACTION11chain 'B' and (resid 200 through 210 )B200 - 210
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 122 )D1 - 122
13X-RAY DIFFRACTION13chain 'D' and (resid 123 through 217 )D123 - 217
14X-RAY DIFFRACTION14chain 'E' and (resid 1 through 19 )E1 - 19
15X-RAY DIFFRACTION15chain 'E' and (resid 20 through 74 )E20 - 74
16X-RAY DIFFRACTION16chain 'E' and (resid 75 through 115 )E75 - 115
17X-RAY DIFFRACTION17chain 'E' and (resid 116 through 199 )E116 - 199
18X-RAY DIFFRACTION18chain 'E' and (resid 200 through 210 )E200 - 210
19X-RAY DIFFRACTION19chain 'F' and (resid 28 through 34 )F28 - 34
20X-RAY DIFFRACTION20chain 'F' and (resid 35 through 52 )F35 - 52
21X-RAY DIFFRACTION21chain 'F' and (resid 53 through 62 )F53 - 62
22X-RAY DIFFRACTION22chain 'F' and (resid 63 through 76 )F63 - 76
23X-RAY DIFFRACTION23chain 'F' and (resid 77 through 84 )F77 - 84
24X-RAY DIFFRACTION24chain 'F' and (resid 85 through 109 )F85 - 109
25X-RAY DIFFRACTION25chain 'F' and (resid 110 through 139 )F110 - 139
26X-RAY DIFFRACTION26chain 'F' and (resid 140 through 149 )F140 - 149
27X-RAY DIFFRACTION27chain 'F' and (resid 150 through 160 )F150 - 160
28X-RAY DIFFRACTION28chain 'C' and (resid 26 through 62 )C26 - 62
29X-RAY DIFFRACTION29chain 'C' and (resid 63 through 84 )C63 - 84
30X-RAY DIFFRACTION30chain 'C' and (resid 85 through 109 )C85 - 109
31X-RAY DIFFRACTION31chain 'C' and (resid 110 through 139 )C110 - 139
32X-RAY DIFFRACTION32chain 'C' and (resid 140 through 149 )C140 - 149
33X-RAY DIFFRACTION33chain 'C' and (resid 150 through 168 )C150 - 168

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