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- PDB-3u36: Crystal Structure of PG9 Fab -

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Basic information

Entry
Database: PDB / ID: 3u36
TitleCrystal Structure of PG9 Fab
Components
  • PG9 Fab heavy chain
  • PG9 Fab light chain
KeywordsIMMUNE SYSTEM / immunoglobulin / gp120 binding
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.281 Å
AuthorsMcLellan, J.S. / Kwong, P.D.
CitationJournal: Nature / Year: 2011
Title: Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.
Authors: McLellan, J.S. / Pancera, M. / Carrico, C. / Gorman, J. / Julien, J.P. / Khayat, R. / Louder, R. / Pejchal, R. / Sastry, M. / Dai, K. / O'Dell, S. / Patel, N. / Shahzad-Ul-Hussan, S. / Yang, ...Authors: McLellan, J.S. / Pancera, M. / Carrico, C. / Gorman, J. / Julien, J.P. / Khayat, R. / Louder, R. / Pejchal, R. / Sastry, M. / Dai, K. / O'Dell, S. / Patel, N. / Shahzad-Ul-Hussan, S. / Yang, Y. / Zhang, B. / Zhou, T. / Zhu, J. / Boyington, J.C. / Chuang, G.Y. / Diwanji, D. / Georgiev, I. / Do Kwon, Y. / Lee, D. / Louder, M.K. / Moquin, S. / Schmidt, S.D. / Yang, Z.Y. / Bonsignori, M. / Crump, J.A. / Kapiga, S.H. / Sam, N.E. / Haynes, B.F. / Burton, D.R. / Koff, W.C. / Walker, L.M. / Phogat, S. / Wyatt, R. / Orwenyo, J. / Wang, L.X. / Arthos, J. / Bewley, C.A. / Mascola, J.R. / Nabel, G.J. / Schief, W.R. / Ward, A.B. / Wilson, I.A. / Kwong, P.D.
History
DepositionOct 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: PG9 Fab heavy chain
L: PG9 Fab light chain
A: PG9 Fab heavy chain
B: PG9 Fab light chain
C: PG9 Fab heavy chain
D: PG9 Fab light chain
E: PG9 Fab heavy chain
F: PG9 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,12614
Polymers199,5498
Non-polymers5766
Water0
1
H: PG9 Fab heavy chain
L: PG9 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0794
Polymers49,8872
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-45 kcal/mol
Surface area19580 Å2
MethodPISA
2
A: PG9 Fab heavy chain
B: PG9 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0794
Polymers49,8872
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-43 kcal/mol
Surface area19560 Å2
MethodPISA
3
C: PG9 Fab heavy chain
D: PG9 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9833
Polymers49,8872
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-32 kcal/mol
Surface area19580 Å2
MethodPISA
4
E: PG9 Fab heavy chain
F: PG9 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9833
Polymers49,8872
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-32 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.594, 81.038, 91.691
Angle α, β, γ (deg.)107.23, 90.13, 107.96
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain H and (resseq 2:103 or resseq 117:150 or resseq 152:231 )
211chain A and (resseq 2:103 or resseq 117:150 or resseq 152:231 )
311chain C and (resseq 2:103 or resseq 117:150 or resseq 152:231 )
411chain E and (resseq 2:103 or resseq 117:150 or resseq 152:231 )
112chain L and (resseq 0:210 )
212chain B and (resseq 0:210 )
312chain D and (resseq 0:210 )
412chain F and (resseq 0:210 )

NCS ensembles :
ID
1
2

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Components

#1: Antibody
PG9 Fab heavy chain


Mass: 27050.076 Da / Num. of mol.: 4 / Fragment: antigen-binding fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293S / Production host: Homo sapiens (human)
#2: Antibody
PG9 Fab light chain


Mass: 22837.256 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293S / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4

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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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% (w/v) PEG 3350, 15% (v/v) 2-methyl-2,4-pentanediol, 0.2 M lithium sulfate, 0.1 M imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 24, 2011
RadiationMonochromator: Si220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 28094 / Num. obs: 25060 / % possible obs: 89.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 1.87 / Num. unique all: 2071 / % possible all: 73.1

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3LRS

3lrs


Resolution: 3.281→38.485 Å / SU ML: 0.72 / σ(F): 1.97 / Phase error: 29.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 1268 5.07 %RANDOM
Rwork0.2145 ---
obs0.2162 24997 87.75 %-
all-28486 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.985 Å2 / ksol: 0.291 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.6383 Å222.2372 Å2-14.2427 Å2
2--29.288 Å211.1829 Å2
3----15.6497 Å2
Refinement stepCycle: LAST / Resolution: 3.281→38.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12824 0 30 0 12854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413172
X-RAY DIFFRACTIONf_angle_d0.917909
X-RAY DIFFRACTIONf_dihedral_angle_d11.1064669
X-RAY DIFFRACTIONf_chiral_restr0.0612003
X-RAY DIFFRACTIONf_plane_restr0.0042286
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11H1642X-RAY DIFFRACTIONPOSITIONAL
12A1642X-RAY DIFFRACTIONPOSITIONAL0.02
13C1642X-RAY DIFFRACTIONPOSITIONAL0.021
14E1634X-RAY DIFFRACTIONPOSITIONAL0.022
21L1566X-RAY DIFFRACTIONPOSITIONAL
22B1566X-RAY DIFFRACTIONPOSITIONAL0.028
23D1566X-RAY DIFFRACTIONPOSITIONAL0.023
24F1566X-RAY DIFFRACTIONPOSITIONAL0.029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2814-3.41270.34951080.30071873X-RAY DIFFRACTION62
3.4127-3.5680.3371350.282349X-RAY DIFFRACTION79
3.568-3.75590.2861260.23992504X-RAY DIFFRACTION83
3.7559-3.9910.28451190.22212671X-RAY DIFFRACTION88
3.991-4.29880.24991690.18362727X-RAY DIFFRACTION92
4.2988-4.73070.21971460.16552854X-RAY DIFFRACTION95
4.7307-5.41360.20231580.17532892X-RAY DIFFRACTION96
5.4136-6.81440.24251350.21472969X-RAY DIFFRACTION98
6.8144-38.48760.23991720.24072890X-RAY DIFFRACTION97
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)
13.4796-0.96621.45024.00772.02689.45440.0599-0.1456-0.5883-0.1686-0.11830.13560.8981-0.11450.13330.4586-0.11090.00080.46360.1970.69021.829529.04057.1476
24.1661-0.9463-1.42424.912-1.28983.2795-1.0652-1.29380.64930.73391.28990.1175-0.4969-0.7789-0.12571.10480.7082-0.15271.4585-0.32470.9632-9.465465.845118.4318
32.41520.76570.65953.6232-1.32554.7445-0.11140.5185-0.0728-0.35250.1827-0.07710.54930.3629-0.04610.50950.3648-0.05960.9341-0.18110.169221.253448.4804-52.1609
44.77912.41020.95682.25941.19152.3397-1.33160.27171.34940.4398-0.2931-0.778-0.9991.14060.59141.1057-0.2732-0.75831.04060.48471.801632.65884.8025-39.5312
56.2341-0.4741-2.58684.60880.47268.4344-0.16320.16710.98970.02080.01350.1511-0.70860.58580.16960.443-0.0602-0.05270.58890.10820.746237.700958.4032-0.6683
69.55512.8854-0.52067.9274-1.85354.8245-0.4565-0.0988-1.353-0.50940.4949-0.30130.26360.2022-0.0460.66120.0434-0.09920.825-0.33150.903126.122921.8289-12.3829
74.38072.8904-1.66539.167-3.19823.19880.26550.14980.30690.3839-0.293-0.1466-0.4322-0.320.03630.71410.19170.01440.9542-0.08590.4332-14.555367.3843-28.4067
85.5774-1.9363-3.77774.43852.66165.1053-0.5366-0.5483-0.80690.9130.26170.6983-0.15750.19040.11280.88260.5168-0.00670.65590.06640.899-2.800331.289-40.835
96.7248-5.22611.05927.4947-2.56325.59550.2244-0.191-0.0826-0.2004-0.02150.03410.7460.0249-0.17470.6609-0.1106-0.08980.63910.02760.3839-3.95638.9904-11.0989
104.4687-1.74720.13914.98031.90058.0604-0.5375-0.04360.27420.24450.3864-1.4675-1.25420.49980.14160.518-0.0858-0.05680.5850.1210.99940.024666.65174.3003
113.2958-0.46232.45173.05320.88825.30040.34010.6069-0.1535-0.0838-0.28160.03040.54790.17960.01590.71870.1428-0.04680.85020.0240.356327.068645.6832-31.5666
127.6999-0.71962.07649.4739-0.29276.374-0.6045-0.40330.52370.5709-0.35811.1492-1.4898-0.70690.9970.79120.209-0.07111.2074-0.00230.948622.939577.0973-27.8439
135.2982.6602-1.8986.3053-3.24714.6905-0.0078-0.59520.09090.24390.17930.1211-0.3310.1838-0.18640.56270.00830.04370.70010.00250.249431.848848.279117.4791
148.7714-1.1237-2.89525.91.93323.8283-0.2216-0.6403-1.333-0.17640.1165-0.71581.43740.99070.07690.85340.1693-0.17911.01210.0761.042335.768320.73471.8597
154.9545-1.0122-4.88972.33921.85397.00450.186-0.77430.07370.09970.30450.2704-0.4859-0.2628-0.54180.6910.04090.05980.91820.25840.4931-8.73370.2225-49.1403
164.56721.9552-2.01287.6853-2.27422.6602-0.52840.063-0.6295-0.15180.60080.75680.48-0.7918-0.04530.74970.1372-0.11591.14760.26751.028-12.430538.7718-53.0448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain H and resid 1:135
2X-RAY DIFFRACTION2chain H and resid 136:232
3X-RAY DIFFRACTION3chain A and resid 1:135
4X-RAY DIFFRACTION4chain A and resid 136:232
5X-RAY DIFFRACTION5chain C and resid 1:135
6X-RAY DIFFRACTION6chain C and resid 136:232
7X-RAY DIFFRACTION7chain E and resid 1:135
8X-RAY DIFFRACTION8chain E and resid 136:232
9X-RAY DIFFRACTION9chain L and resid 1:110
10X-RAY DIFFRACTION10chain L and resid 111:210
11X-RAY DIFFRACTION11chain B and resid 1:110
12X-RAY DIFFRACTION12chain B and resid 111:210
13X-RAY DIFFRACTION13chain D and resid 1:110
14X-RAY DIFFRACTION14chain D and resid 111:210
15X-RAY DIFFRACTION15chain F and resid 1:110
16X-RAY DIFFRACTION16chain F and resid 111:210

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