PDB-6h1e: Crystal structure of C21orf127-TRMT112 in complex with SAH and H4...

ID or keywords:

Entry

Database: PDB / ID: 6h1e

Title

Crystal structure of C21orf127-TRMT112 in complex with SAH and H4 peptide

Components

HemK methyltransferase family member 2
Histone H4 peptide
Multifunctional methyltransferase subunit TRM112-like protein

Keywords

GENE REGULATION / protein methyltransferase / histone methylation / complex / SAH

Function / homology

Function and homology information

histone H4K12 methyltransferase activity / arsonoacetate metabolic process / arsenite methyltransferase activity / protein-glutamine N-methyltransferase activity / eRF1 methyltransferase complex / peptidyl-glutamine methylation / tRNA (m2G10) methyltransferase complex / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / toxin metabolic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Wang, S. / Hermann, B. / Metzger, E. / Peng, L. / Einsle, O. / Schuele, R.

Funding support

Germany, 2items

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2019
Title: KMT9 monomethylates histone H4 lysine 12 and controls proliferation of prostate cancer cells.
Authors: Metzger, E. / Wang, S. / Urban, S. / Willmann, D. / Schmidt, A. / Offermann, A. / Allen, A. / Sum, M. / Obier, N. / Cottard, F. / Ulferts, S. / Preca, B.T. / Hermann, B. / Maurer, J. / ...

History

Deposition	Jul 11, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 22, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6h1e.cif.gz	172.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6h1e.ent.gz	112 KB	Display	PDB format
PDBx/mmJSON format	6h1e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6h1e_validation.pdf.gz	744.2 KB	Display	wwPDB validaton report
Full document	6h1e_full_validation.pdf.gz	745.3 KB	Display
Data in XML	6h1e_validation.xml.gz	14.5 KB	Display
Data in CIF	6h1e_validation.cif.gz	19.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h1/6h1e ftp://data.pdbj.org/pub/pdb/validation_reports/h1/6h1e	HTTPS FTP

-
Related structure data

Related structure data	6h1dSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6khs-d 1kc1-d 4gfi-4 1fhf-1 1sqh-d 3bkz-d 3tmd-d 6l8l-3 6kmr-d 7atj-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#60 - Dec 2004 Ubiquitin similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: HemK methyltransferase family member 2

B: Multifunctional methyltransferase subunit TRM112-like protein

S: Histone H4 peptide

hetero molecules

39.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: isothermal titration calorimetry

Unit cell

Length a, b, c (Å)	71.231, 71.231, 130.808
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	94
Space group name H-M	P4₂2₁2
Space group name Hall	P4n2n
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+1/2 #3: y+1/2,-x+1/2,z+1/2 #4: x+1/2,-y+1/2,-z+1/2 #5: -x+1/2,y+1/2,-z+1/2 #6: -x,-y,z #7: y,x,-z #8: -y,-x,-z

#1: Protein	HemK methyltransferase family member 2 / M.HsaHemK2P / N(6)-adenine-specific DNA methyltransferase 1 Mass: 22344.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: N6AMT1, C21orf127, HEMK2, PRED28 / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y5N5, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein	Multifunctional methyltransferase subunit TRM112-like protein / tRNA methyltransferase 112 homolog Mass: 14272.412 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT112, AD-001, HSPC152, HSPC170 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UI30
#3: Protein/peptide	Histone H4 peptide Mass: 2113.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 46.97 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 1.1-1.3 M Sodium Citrate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 9, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→48.18 Å / Num. obs: 27384 / % possible obs: 99.96 % / Redundancy: 22.5 % / B_iso Wilson estimate: 28.55 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.187 / R_pim(I) all: 0.056 / Net I/σ(I): 1.2
Reflection shell	Resolution: 1.9→1.97 Å / Redundancy: 21.9 % / R_merge(I) obs: 2.74 / CC_1/2: 0.296 / R_pim(I) all: 0.857 / % possible all: 99.89

-
Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6H1D

6h1d

Resolution: 1.9→47 Å / SU ML: 0.2703 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.2871

	R_factor	Num. reflection	% reflection
R_free	0.2445	1349	4.94 %
R_work	0.1959	-	-
obs	0.1983	27325	99.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 35.97 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2508	0	26	74	2608

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0074	2587
X-RAY DIFFRACTION	f_angle_d	0.9166	3510
X-RAY DIFFRACTION	f_chiral_restr	0.0548	404
X-RAY DIFFRACTION	f_plane_restr	0.0056	454
X-RAY DIFFRACTION	f_dihedral_angle_d	7.2391	1564

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9-1.97	0.3772	116	0.3463	2549	X-RAY DIFFRACTION	99.89
1.97-2.05	0.3032	113	0.2958	2577	X-RAY DIFFRACTION	100
2.05-2.14	0.294	147	0.2629	2521	X-RAY DIFFRACTION	99.96
2.14-2.25	0.2766	142	0.236	2552	X-RAY DIFFRACTION	100
2.25-2.39	0.2984	120	0.218	2574	X-RAY DIFFRACTION	100
2.39-2.58	0.2594	133	0.2041	2583	X-RAY DIFFRACTION	100
2.58-2.84	0.2828	135	0.2088	2571	X-RAY DIFFRACTION	100
2.84-3.25	0.24	146	0.2007	2619	X-RAY DIFFRACTION	100
3.25-4.09	0.2116	149	0.1601	2616	X-RAY DIFFRACTION	99.96
4.09-47.02	0.2073	148	0.1573	2814	X-RAY DIFFRACTION	99.97

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	9.35032809718	-4.03963936812	0.221447055784	3.39284313986	-0.0832218449617	0.0215892753684	0.985017755419	0.543171032284	-0.438311938208	-0.641432644856	0.26230781848	-0.91827211254	0.61325842979	0.425547932855	-0.1853018245	0.895757938746	-0.095499397506	0.00371843162442	0.754667516976	-0.218919085527	0.53101383229	-7.51536222617	-20.8497623913	-25.0821559971
2	2.28327538753	1.07092026013	-1.3776795898	3.4389582235	0.990259683979	2.38713335727	0.0305043713697	0.124366017576	0.203618511466	-0.429929084572	0.169203710216	-1.16191586252	-0.126548205191	1.30540604091	-0.133896849669	0.406741894491	-0.0815129434909	0.0591084428297	0.612034096034	-0.132337553199	0.501627117419	-2.99062547676	-10.2833833071	-21.1700486567
3	1.90697879574	-0.715604670278	-0.153790745237	2.7633478292	1.1771447664	1.81817563309	0.0888959526122	0.329936892499	0.0574548023289	-0.672459876181	0.0538161970432	-0.296710664786	-0.474093817128	0.120423166712	-0.0532179672449	0.400974146044	-0.0507774327094	0.0310054131578	0.226420214613	-0.00162950704692	0.174935567284	-15.1560456578	-4.66402448993	-22.6427134804
4	0.586915115342	-0.987447710658	-0.194606247025	1.85887083598	0.670551517691	2.19154612002	0.176094266528	0.183465110982	0.0371511363095	-0.506429046761	-0.0802421358311	0.204241400709	-0.110436542113	-0.110829857442	0.00807188419897	0.228796968754	-0.0344841588044	-0.0328177383776	0.152220335059	-0.00595680489877	0.223561107711	-20.8333572274	-9.72781277313	-16.5934351528
5	0.556862604608	-0.679323354592	-0.233498206087	1.41742223094	-0.470046761125	2.00024052478	0.0435154711645	0.23554744873	-0.42613177027	0.0905620409243	0.0726604147713	0.109883683873	0.603075820129	0.19789540489	-0.0806488036132	0.394879865866	0.00239550906851	-0.022082600112	0.253271086328	-0.093386273943	0.299669543628	-15.4011017001	-26.3567302905	-17.5183986
6	2.47399882774	0.173022099769	-0.0529879868402	1.30561047289	0.347544263496	2.22239966101	0.0933190816308	0.343048965687	-0.0942311373414	-0.335222894753	-0.130638045395	0.21410159492	0.0605604661197	-0.341856776085	0.0527567106703	0.329545711667	-0.028629148436	-0.0899026175523	0.286258444354	-0.0563495882159	0.286124962831	-26.42488431	-15.5897378464	-23.2085596125
7	0.506219131166	-0.747557278618	-0.771300548706	4.09668928641	1.4393712714	1.24547118046	-0.260143524859	0.618619975962	-0.590109388794	-0.0982733110286	0.204083981153	1.10765427406	0.361453422997	-0.170508791941	0.188715243004	0.459701070811	-0.0681258400812	-0.19592292101	0.51938386694	-0.0923901788105	0.450868126063	-31.4925377533	-21.6708343537	-29.7926863277
8	2.0617325682	-0.688972083639	-0.369652130847	2.58903250159	1.44792930847	2.86582248243	0.403879225616	0.361294202643	-0.212579154907	-0.660362606719	-0.260848991408	0.207141823377	-0.14728465552	-0.235317047627	0.0162814766378	0.454596091333	-0.0184937982923	-0.0898254539462	0.426635721497	-0.0750542029775	0.239549219145	-23.1959102927	-16.1188166258	-32.8612073683
9	1.11948598393	-0.487407802837	0.505914625128	2.7690965548	-0.178434174534	2.19888668303	-0.271543922795	0.190518818982	0.151546800007	-0.168432700877	0.138122128715	0.167868190526	0.223245054493	-0.0562817879209	-0.0165023051516	0.163586077117	0.000574492130563	-0.0439752298246	0.165000549984	-0.00131816214699	0.262920644482	-21.5492860444	1.73134632221	-6.26069197655
10	1.63455104157	-0.405834265912	0.881038312664	3.19231998945	-0.0572638705086	2.70819222051	-0.0710531217062	-0.240004530778	-0.258303919059	0.183349692444	0.181706002192	0.220556492272	0.375705935138	-0.364510494616	-0.01768900856	0.175716887231	-0.0268322350126	0.00487562039263	0.187389313908	0.0350817486672	0.24110208783	-22.028128745	-4.13226260371	0.857415958254
11	3.28617340286	-0.628896621356	0.517041918476	2.77935261937	-0.258542860414	1.92754579879	0.0966330375983	0.447651333217	0.0688881122237	-0.16545698205	-0.0282772237258	0.198091489676	-0.042577069176	0.121685142049	-0.00159207943112	0.284952092631	0.00407277684213	-0.060617465308	0.253996552849	0.0377455588516	0.240882080895	-22.2892926772	10.0189731654	-14.2047213323
12	1.80540208749	-0.300612596258	-0.337313824495	3.01723423717	-0.0732621996852	2.30099609339	-0.0778345993745	-0.341891074196	0.539960355485	0.14342629805	0.0633328994399	0.376532430077	-0.45232363023	-0.451097902047	-0.0359450536181	0.170863851785	0.064296649555	-0.0450049280264	0.204097122991	-0.0453456011691	0.350840396474	-25.5669037894	11.5473800737	0.0856460234361
13	3.66121185868	-0.427584047914	0.663839850279	2.83328131672	-0.405989505239	1.6244838643	-0.0767608157397	0.0452852482977	0.318874149373	-0.56363567728	0.234756627718	0.447545062036	-0.189802544508	-0.290944734061	0.0784001955592	0.257920993994	-0.0151420268372	-0.102864780085	0.19842906297	0.067396998154	0.327358848762	-22.8969622261	16.4236429067	-10.7053942914
14	1.21788575683	-0.322718008088	0.228924189448	3.09004467425	-0.673134781523	1.10497463268	-0.223797457762	-0.0645548967637	-0.0586372842759	0.020789471315	0.133720900657	-0.0207832541773	-0.163700550849	-0.000210911286042	0.0469193631487	0.158614464253	-0.00595000408865	-0.0317429874407	0.183231389859	-0.020118292058	0.23771771021	-14.7043923037	0.430873897878	-0.469572646153
15	6.10203823599	1.22000208136	-3.1885367692	2.79264802549	-1.14103946861	3.62538142508	-0.118445800083	-0.0600603451398	-0.0998969531708	-0.137773581024	0.27320233496	0.894145545917	0.0803100597475	-0.379355739143	0.0147294412348	0.147050528607	-0.0210226428417	0.0102549916128	0.267126210886	0.0860832044278	0.367479495429	-22.7758695273	-9.52040627216	4.06142371821
16	3.89289665172	0.602388125423	1.05540353782	5.94522598117	0.458461250193	3.16745026226	0.165917319253	-0.040611020424	-0.592561001794	0.0642943116276	-0.231801992848	0.0955424336069	0.589586299976	0.108464986916	0.0165010350697	0.256186889425	-0.0307659021202	0.0197243675316	0.20360198908	-0.0080082551326	0.266249674685	-14.6576429381	-9.3753871946	-4.13613241637

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'S' and (resid 11 through 15 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 7 through 26 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 27 through 92 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 93 through 129 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 130 through 149 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 150 through 177 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 178 through 188 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 189 through 213 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 2 through 9 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 10 through 33 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 34 through 51 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 52 through 74 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 75 through 90 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 91 through 100 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 101 through 110 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 111 through 119 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi